1
|
Quaiyum S, Sun J, Marchand V, Sun G, Reed CJ, Motorin Y, Dedon PC, Minnick MF, de Crécy-Lagard V. Mapping the tRNA modification landscape of Bartonella henselae Houston I and Bartonella quintana Toulouse. Front Microbiol 2024; 15:1369018. [PMID: 38544857 PMCID: PMC10965804 DOI: 10.3389/fmicb.2024.1369018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 02/26/2024] [Indexed: 04/04/2024] Open
Abstract
Transfer RNA (tRNA) modifications play a crucial role in maintaining translational fidelity and efficiency, and they may function as regulatory elements in stress response and virulence. Despite their pivotal roles, a comprehensive mapping of tRNA modifications and their associated synthesis genes is still limited, with a predominant focus on free-living bacteria. In this study, we employed a multidisciplinary approach, incorporating comparative genomics, mass spectrometry, and next-generation sequencing, to predict the set of tRNA modification genes responsible for tRNA maturation in two intracellular pathogens-Bartonella henselae Houston I and Bartonella quintana Toulouse, which are causative agents of cat-scratch disease and trench fever, respectively. This analysis presented challenges, particularly because of host RNA contamination, which served as a potential source of error. However, our approach predicted 26 genes responsible for synthesizing 23 distinct tRNA modifications in B. henselae and 22 genes associated with 23 modifications in B. quintana. Notably, akin to other intracellular and symbiotic bacteria, both Bartonella species have undergone substantial reductions in tRNA modification genes, mostly by simplifying the hypermodifications present at positions 34 and 37. Bartonella quintana exhibited the additional loss of four modifications and these were linked to examples of gene decay, providing snapshots of reductive evolution.
Collapse
Affiliation(s)
- Samia Quaiyum
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, United States
| | - Jingjing Sun
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
| | - Virginie Marchand
- Université de Lorraine, UAR2008/US40 IBSLor, EpiRNA-Seq Core Facility and UMR7365 IMoPA, CNRS-Inserm, Biopôle UL, Nancy, France
| | - Guangxin Sun
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Colbie J. Reed
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, United States
| | - Yuri Motorin
- Université de Lorraine, UAR2008/US40 IBSLor, EpiRNA-Seq Core Facility and UMR7365 IMoPA, CNRS-Inserm, Biopôle UL, Nancy, France
| | - Peter C. Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
| | - Michael F. Minnick
- Division of Biological Sciences, University of Montana, Missoula, MT, United States
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, United States
- Genetic Institute, University of Florida, Gainesville, FL, United States
| |
Collapse
|
2
|
Quaiyum S, Sun J, Marchand V, Sun G, Reed CJ, Motorin Y, Dedon PC, Minnick MF, de Crécy-Lagard V. Mapping the tRNA Modification Landscape of Bartonella henselae Houston I and Bartonella quintana Toulouse. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.08.574729. [PMID: 38260440 PMCID: PMC10802484 DOI: 10.1101/2024.01.08.574729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Transfer RNA (tRNA) modifications play a crucial role in maintaining translational fidelity and efficiency, and they may function as regulatory elements in stress response and virulence. Despite their pivotal roles, a comprehensive mapping of tRNA modifications and their associated synthesis genes is still limited, with a predominant focus on free-living bacteria. In this study, we employed a multidisciplinary approach, incorporating comparative genomics, mass spectrometry, and next-generation sequencing, to predict the set of tRNA modification genes responsible for tRNA maturation in two intracellular pathogens- Bartonella henselae Houston I and Bartonella quintana Toulouse, which are causative agents of cat-scratch disease and trench fever, respectively. This analysis presented challenges, particularly because of host RNA contamination, which served as a potential source of error. However, our approach predicted 26 genes responsible for synthesizing 23 distinct tRNA modifications in B. henselae and 22 genes associated with 23 modifications in B. quintana . Notably, akin to other intracellular and symbiotic bacteria, both Bartonella species have undergone substantial reductions in tRNA modification genes, mostly by simplifying the hypermodifications present at positions 34 and 37. B. quintana exhibited the additional loss of four modifications and these were linked to examples of gene decay, providing snapshots of reductive evolution.
Collapse
|
3
|
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
|
4
|
Kotammagari TK, Tähtinen P, Lönnberg T. Oligonucleotides Featuring a Covalently Mercurated 6-Phenylcarbazole Residue as High-Affinity Hybridization Probes for Thiopyrimidine-Containing Sequences. Chemistry 2022; 28:e202202530. [PMID: 36108095 PMCID: PMC10092508 DOI: 10.1002/chem.202202530] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Indexed: 12/14/2022]
Abstract
Short oligonucleotides incorporating either 1-mercuri-6-phenylcarbazole, 8-mercuri-6-phenylcarbazole, or 1,8-dimercuri-6-phenylcarbazole C-nucleoside in the middle of the chain have been synthesized and studied for their potential as hybridization probes for sequences containing thiopyrimidine nucleobases. All of these oligonucleotides formed very stable duplexes with complementary sequences pairing the organometallic moiety with either 2- or 4-thiothymine. The isomeric monomercurated oligonucleotides were also able to discriminate between 2- and 4-thiothymine based on the different melting temperatures of the respective duplexes. DFT-optimized structures of the most stable mononuclear HgII -mediated base pairs featured a coordinated covalent bond between HgII and either S2 or S4 and a hydrogen bond between the carbazole nitrogen and N3. The dinuclear HgII -mediated base pairs, in turn, were geometrically very similar to the one previously reported to form between 1,8-dimercuri-6-phenylcarbazole and thymine and had one HgII ion coordinated to a thio and the other one to an oxo substituent.
Collapse
Affiliation(s)
- Tharun K Kotammagari
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
| | - Petri Tähtinen
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
| | - Tuomas Lönnberg
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
| |
Collapse
|
5
|
Arzumanian VA, Dolgalev GV, Kurbatov IY, Kiseleva OI, Poverennaya EV. Epitranscriptome: Review of Top 25 Most-Studied RNA Modifications. Int J Mol Sci 2022; 23:ijms232213851. [PMID: 36430347 PMCID: PMC9695239 DOI: 10.3390/ijms232213851] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/12/2022] Open
Abstract
The alphabet of building blocks for RNA molecules is much larger than the standard four nucleotides. The diversity is achieved by the post-transcriptional biochemical modification of these nucleotides into distinct chemical entities that are structurally and functionally different from their unmodified counterparts. Some of these modifications are constituent and critical for RNA functions, while others serve as dynamic markings to regulate the fate of specific RNA molecules. Together, these modifications form the epitranscriptome, an essential layer of cellular biochemistry. As of the time of writing this review, more than 300 distinct RNA modifications from all three life domains have been identified. However, only a few of the most well-established modifications are included in most reviews on this topic. To provide a complete overview of the current state of research on the epitranscriptome, we analyzed the extent of the available information for all known RNA modifications. We selected 25 modifications to describe in detail. Summarizing our findings, we describe the current status of research on most RNA modifications and identify further developments in this field.
Collapse
Affiliation(s)
- Viktoriia A. Arzumanian
- Correspondence: (V.A.A.); (G.V.D.); Tel.: +7-960-889-7117 (V.A.A.); +7-967-236-36-79 (G.V.D.)
| | - Georgii V. Dolgalev
- Correspondence: (V.A.A.); (G.V.D.); Tel.: +7-960-889-7117 (V.A.A.); +7-967-236-36-79 (G.V.D.)
| | | | | | | |
Collapse
|
6
|
Prediction of the Iron–Sulfur Binding Sites in Proteins Using the Highly Accurate Three-Dimensional Models Calculated by AlphaFold and RoseTTAFold. INORGANICS 2021. [DOI: 10.3390/inorganics10010002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
AlphaFold and RoseTTAFold are deep learning-based approaches that predict the structure of proteins from their amino acid sequences. Remarkable success has recently been achieved in the prediction accuracy of not only the fold of the target protein but also the position of its amino acid side chains. In this article, I question the accuracy of these methods to predict iron–sulfur binding sites. I analyze three-dimensional models calculated by AlphaFold and RoseTTAFold of Fe–S–dependent enzymes, for which no structure of a homologous protein has been solved experimentally. In all cases, the amino acids that presumably coordinate the cluster were gathered together and facing each other, which led to a quite accurate model of the Fe–S cluster binding site. Yet, cysteine candidates were often involved in intramolecular disulfide bonds, and the number and identity of the protein amino acids that should ligate the cluster were not always clear. The experimental structure determination of the protein with its Fe–S cluster and in complex with substrate/inhibitor/product is still needed to unambiguously visualize the coordination state of the cluster and understand the conformational changes occurring during catalysis.
Collapse
|
7
|
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
|
8
|
Kusnadi EP, Timpone C, Topisirovic I, Larsson O, Furic L. Regulation of gene expression via translational buffering. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1869:119140. [PMID: 34599983 DOI: 10.1016/j.bbamcr.2021.119140] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 09/19/2021] [Accepted: 09/21/2021] [Indexed: 12/28/2022]
Abstract
Translation of an mRNA represents a critical step during the expression of protein-coding genes. As mechanisms governing post-transcriptional regulation of gene expression are progressively unveiled, it is becoming apparent that transcriptional programs are not fully reflected in the proteome. Herein, we highlight a previously underappreciated post-transcriptional mode of regulation of gene expression termed translational buffering. In principle, translational buffering opposes the impact of alterations in mRNA levels on the proteome. We further describe three types of translational buffering: compensation, which maintains protein levels e.g. across species or individuals; equilibration, which retains pathway stoichiometry; and offsetting, which acts as a reversible mechanism that maintains the levels of selected subsets of proteins constant despite genetic alteration and/or stress-induced changes in corresponding mRNA levels. While mechanisms underlying compensation and equilibration have been reviewed elsewhere, the principal focus of this review is on the less-well understood mechanism of translational offsetting. Finally, we discuss potential roles of translational buffering in homeostasis and disease.
Collapse
Affiliation(s)
- Eric P Kusnadi
- Translational Prostate Cancer Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia; Cancer Program, Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
| | - Clelia Timpone
- Translational Prostate Cancer Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Ivan Topisirovic
- Lady Davis Institute, Gerald Bronfman Department of Oncology and Departments of Biochemistry and Experimental Medicine, McGill University, Montreal, QC, Canada.
| | - Ola Larsson
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden.
| | - Luc Furic
- Translational Prostate Cancer Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia; Cancer Program, Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia.
| |
Collapse
|
9
|
Das M, Dewan A, Shee S, Singh A. The Multifaceted Bacterial Cysteine Desulfurases: From Metabolism to Pathogenesis. Antioxidants (Basel) 2021; 10:antiox10070997. [PMID: 34201508 PMCID: PMC8300815 DOI: 10.3390/antiox10070997] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/01/2021] [Accepted: 05/06/2021] [Indexed: 12/02/2022] Open
Abstract
Living cells have developed a relay system to efficiently transfer sulfur (S) from cysteine to various thio-cofactors (iron-sulfur (Fe-S) clusters, thiamine, molybdopterin, lipoic acid, and biotin) and thiolated tRNA. The presence of such a transit route involves multiple protein components that allow the flux of S to be precisely regulated as a function of environmental cues to avoid the unnecessary accumulation of toxic concentrations of soluble sulfide (S2−). The first enzyme in this relay system is cysteine desulfurase (CSD). CSD catalyzes the release of sulfane S from L-cysteine by converting it to L-alanine by forming an enzyme-linked persulfide intermediate on its conserved cysteine residue. The persulfide S is then transferred to diverse acceptor proteins for its incorporation into the thio-cofactors. The thio-cofactor binding-proteins participate in essential and diverse cellular processes, including DNA repair, respiration, intermediary metabolism, gene regulation, and redox sensing. Additionally, CSD modulates pathogenesis, antibiotic susceptibility, metabolism, and survival of several pathogenic microbes within their hosts. In this review, we aim to comprehensively illustrate the impact of CSD on bacterial core metabolic processes and its requirement to combat redox stresses and antibiotics. Targeting CSD in human pathogens can be a potential therapy for better treatment outcomes.
Collapse
|
10
|
Abstract
Iron-Sulfur (Fe-S) clusters function as core prosthetic groups known to modulate the activity of metalloenzymes, act as trafficking vehicles for biological iron and sulfur, and participate in several intersecting metabolic pathways. The formation of these clusters is initiated by a class of enzymes called cysteine desulfurases, whose primary function is to shuttle sulfur from the amino acid L-cysteine to a variety of sulfur transfer proteins involved in Fe-S cluster synthesis as well as in the synthesis of other thiocofactors. Thus, sulfur and Fe-S cluster metabolism are connected through shared enzyme intermediates, and defects in their associated pathways cause a myriad of pleiotropic phenotypes, which are difficult to dissect. Post-transcriptionally modified transfer RNA (tRNA) represents a large class of analytes whose synthesis often requires the coordinated participation of sulfur transfer and Fe-S enzymes. Therefore, these molecules can be used as biologically relevant readouts for cellular Fe and S status. Methods employing LC-MS technology provide a valuable experimental tool to determine the relative levels of tRNA modification in biological samples and, consequently, to assess genetic, nutritional, and environmental factors modulating reactions dependent on Fe-S clusters. Herein, we describe a robust method for extracting RNA and analytically evaluating the degree of Fe-S-dependent and -independent tRNA modifications via an LC-MS platform.
Collapse
Affiliation(s)
- Ashley M Edwards
- Department of Chemistry, Wake Forest University, Winston Salem, NC, USA
| | - Maame A Addo
- Department of Chemistry, Wake Forest University, Winston Salem, NC, USA
| | | |
Collapse
|
11
|
Gregorova P, Sipari NH, Sarin LP. Broad-range RNA modification analysis of complex biological samples using rapid C18-UPLC-MS. RNA Biol 2020; 18:1382-1389. [PMID: 33356826 PMCID: PMC8494288 DOI: 10.1080/15476286.2020.1853385] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Post-transcriptional RNA modifications play an important role in cellular metabolism with homoeostatic disturbances manifesting as a wide repertoire of phenotypes, reduced stress tolerance and translational perturbation, developmental defects, and diseases, such as type II diabetes, leukaemia, and carcinomas. Hence, there has been an intense effort to develop various methods for investigating RNA modifications and their roles in various organisms, including sequencing-based approaches and, more frequently, liquid chromatography–mass spectrometry (LC-MS)-based methods. Although LC-MS offers numerous advantages, such as being highly sensitive and quantitative over a broad detection range, some stationary phase chemistries struggle to resolve positional isomers. Furthermore, the demand for detailed analyses of complex biological samples often necessitates long separation times, hampering sample-to-sample turnover and making multisample analyses time consuming. To overcome this limitation, we have developed an ultra-performance LC-MS (UPLC-MS) method that uses an octadecyl carbon chain (C18)-bonded silica matrix for the efficient separation of 50 modified ribonucleosides, including positional isomers, in a single 9-min sample-to-sample run. To validate the performance and versatility of our method, we analysed tRNA modification patterns of representative microorganisms from each domain of life, namely Archaea (Methanosarcina acetivorans), Bacteria (Pseudomonas syringae), and Eukarya (Saccharomyces cerevisiae). Additionally, our method is flexible and readily applicable for detection and relative quantification using stable isotope labelling and targeted approaches like multiple reaction monitoring (MRM). In conclusion, this method represents a fast and robust tool for broad-range exploration and quantification of ribonucleosides, facilitating future homoeostasis studies of RNA modification in complex biological samples.
Collapse
Affiliation(s)
- Pavlina Gregorova
- RNAcious Laboratory, Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Nina H Sipari
- Viikki Metabolomics Unit, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki Finland
| | - L Peter Sarin
- RNAcious Laboratory, Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| |
Collapse
|
12
|
Bimai O, Arragain S, Golinelli-Pimpaneau B. Structure-based mechanistic insights into catalysis by tRNA thiolation enzymes. Curr Opin Struct Biol 2020; 65:69-78. [PMID: 32652441 DOI: 10.1016/j.sbi.2020.06.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 05/16/2020] [Accepted: 06/04/2020] [Indexed: 12/21/2022]
Abstract
In all domains of life, ribonucleic acid (RNA) maturation includes post-transcriptional chemical modifications of nucleosides. Many sulfur-containing nucleosides have been identified in transfer RNAs (tRNAs), such as the derivatives of 2-thiouridine (s2U), 4-thiouridine (s4U), 2-thiocytidine (s2C), 2-methylthioadenosine (ms2A). These modifications are essential for accurate and efficient translation of the genetic code from messenger RNA (mRNA) for protein synthesis. This review summarizes the recent discoveries concerning the mechanistic and structural characterization of tRNA thiolation enzymes that catalyze the non-redox substitution of oxygen for sulfur in nucleosides. Two mechanisms have been described. One involves persulfide formation on catalytic cysteines, while the other uses a [4Fe-4S] cluster, chelated by three conserved cysteines only, as a sulfur carrier.
Collapse
Affiliation(s)
- Ornella Bimai
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Université Paris Sciences et Lettres, 11 Place Marcelin Berthelot, 75231 Paris cedex 05, France
| | - Simon Arragain
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Université Paris Sciences et Lettres, 11 Place Marcelin Berthelot, 75231 Paris cedex 05, France
| | - Béatrice Golinelli-Pimpaneau
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Université Paris Sciences et Lettres, 11 Place Marcelin Berthelot, 75231 Paris cedex 05, France.
| |
Collapse
|
13
|
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: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [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 Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Agnieszka Ruszkowska
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Charlotte N Kunkler
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Kurtis Breger
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Jacob P Hulewicz
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Matthew C Wang
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Noah A Springer
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Jessica A Brown
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| |
Collapse
|
14
|
A Structural Basis for Restricted Codon Recognition Mediated by 2-thiocytidine in tRNA Containing a Wobble Position Inosine. J Mol Biol 2020; 432:913-929. [PMID: 31945376 DOI: 10.1016/j.jmb.2019.12.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 11/25/2019] [Accepted: 12/05/2019] [Indexed: 11/20/2022]
Abstract
Three of six arginine codons (CGU, CGC, and CGA) are decoded by two Escherichia coli tRNAArg isoacceptors. The anticodon stem and loop (ASL) domains of tRNAArg1 and tRNAArg2 both contain inosine and 2-methyladenosine modifications at positions 34 (I34) and 37 (m2A37). tRNAArg1 is also modified from cytidine to 2-thiocytidine at position 32 (s2C32). The s2C32 modification is known to negate wobble codon recognition of the rare CGA codon by an unknown mechanism, while still allowing decoding of CGU and CGC. Substitution of s2C32 for C32 in the Saccharomyces cerevisiae tRNAIleIAU anticodon stem and loop domain (ASL) negates wobble decoding of its synonymous A-ending codon, suggesting that this function of s2C at position 32 is a generalizable property. X-ray crystal structures of variously modified ASLArg1ICG and ASLArg2ICG constructs bound to cognate and wobble codons on the ribosome revealed the disruption of a C32-A38 cross-loop interaction but failed to fully explain the means by which s2C32 restricts I34 wobbling. Computational studies revealed that the adoption of a spatially broad inosine-adenosine base pair at the wobble position of the codon cannot be maintained simultaneously with the canonical ASL U-turn motif. C32-A38 cross-loop interactions are required for stability of the anticodon/codon interaction in the ribosomal A-site.
Collapse
|
15
|
Reichle VF, Petrov DP, Weber V, Jung K, Kellner S. NAIL-MS reveals the repair of 2-methylthiocytidine by AlkB in E. coli. Nat Commun 2019; 10:5600. [PMID: 31811240 PMCID: PMC6898146 DOI: 10.1038/s41467-019-13565-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 11/14/2019] [Indexed: 01/12/2023] Open
Abstract
RNAs contain post-transcriptional modifications, which fulfill a variety of functions in translation, secondary structure stabilization and cellular stress survival. Here, 2-methylthiocytidine (ms2C) is identified in tRNA of E. coli and P. aeruginosa using NAIL-MS (nucleic acid isotope labeling coupled mass spectrometry) in combination with genetic screening experiments. ms2C is only found in 2-thiocytidine (s2C) containing tRNAs, namely tRNAArgCCG, tRNAArgICG, tRNAArgUCU and tRNASerGCU at low abundances. ms2C is not formed by commonly known tRNA methyltransferases. Instead, we observe its formation in vitro and in vivo during exposure to methylating agents. More than half of the s2C containing tRNA can be methylated to carry ms2C. With a pulse-chase NAIL-MS experiment, the repair mechanism by AlkB dependent sulfur demethylation is demonstrated in vivo. Overall, we describe ms2C as a bacterial tRNA modification and damage product. Its repair by AlkB and other pathways is demonstrated in vivo by our powerful NAIL-MS approach. Bacterial tRNA is modified by thiolation of nucleosides. Here the authors identify 2-methylthiocytidine in bacterial tRNA using nucleic acid isotope labeling coupled mass spectrometry. Exposure to methylating agents converts 2-thiocytidine to 2-methylthiocytidine, which is repaired by demethylase AlkB in vivo.
Collapse
Affiliation(s)
- Valentin F Reichle
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany
| | - Dimitar P Petrov
- Department of Biology, Ludwig-Maximilians-University Munich, Grosshaderner Str. 2-4, 82152, Martinsried, Germany
| | - Verena Weber
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany
| | - Kirsten Jung
- Department of Biology, Ludwig-Maximilians-University Munich, Grosshaderner Str. 2-4, 82152, Martinsried, Germany
| | - Stefanie Kellner
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany.
| |
Collapse
|
16
|
Distinct Modified Nucleosides in tRNA Trp from the Hyperthermophilic Archaeon Thermococcus kodakarensis and Requirement of tRNA m 2G10/m 2 2G10 Methyltransferase (Archaeal Trm11) for Survival at High Temperatures. J Bacteriol 2019; 201:JB.00448-19. [PMID: 31405913 DOI: 10.1128/jb.00448-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 08/09/2019] [Indexed: 12/19/2022] Open
Abstract
tRNA m2G10/m2 2G10 methyltransferase (archaeal Trm11) methylates the 2-amino group in guanosine at position 10 in tRNA and forms N 2,N 2-dimethylguanosine (m2 2G10) via N 2-methylguanosine (m2G10). We determined the complete sequence of tRNATrp, one of the substrate tRNAs for archaeal Trm11 from Thermococcus kodakarensis, a hyperthermophilic archaeon. Liquid chromatography/mass spectrometry following enzymatic digestion of tRNATrp identified 15 types of modified nucleoside at 21 positions. Several modifications were found at novel positions in tRNA, including 2'-O-methylcytidine at position 6, 2-thiocytidine at position 17, 2'-O-methyluridine at position 20, 5,2'-O-dimethylcytidine at position 32, and 2'-O-methylguanosine at position 42. Furthermore, methylwyosine was found at position 37 in this tRNATrp, although 1-methylguanosine is generally found at this location in tRNATrp from other archaea. We constructed trm11 (Δtrm11) and some gene disruptant strains and compared their tRNATrp with that of the wild-type strain, which confirmed the absence of m2 2G10 and other corresponding modifications, respectively. The lack of 2-methylguanosine (m2G) at position 67 in the trm11 trm14 double disruptant strain suggested that this methylation is mediated by Trm14, which was previously identified as an m2G6 methyltransferase. The Δtrm11 strain grew poorly at 95°C, indicating that archaeal Trm11 is required for T. kodakarensis survival at high temperatures. The m2 2G10 modification might have effects on stabilization of tRNA and/or correct folding of tRNA at the high temperatures. Collectively, these results provide new clues to the function of modifications and the substrate specificities of modification enzymes in archaeal tRNA, enabling us to propose a strategy for tRNA stabilization of this archaeon at high temperatures.IMPORTANCE Thermococcus kodakarensis is a hyperthermophilic archaeon that can grow at 60 to 100°C. The sequence of tRNATrp from this archaeon was determined by liquid chromatography/mass spectrometry. Fifteen types of modified nucleoside were observed at 21 positions, including 5 modifications at novel positions; in addition, methylwyosine at position 37 was newly observed in an archaeal tRNATrp The construction of trm11 (Δtrm11) and other gene disruptant strains confirmed the enzymes responsible for modifications in this tRNA. The lack of 2-methylguanosine (m2G) at position 67 in the trm11 trm14 double disruptant strain suggested that this position is methylated by Trm14, which was previously identified as an m2G6 methyltransferase. The Δtrm11 strain grew poorly at 95°C, indicating that archaeal Trm11 is required for T. kodakarensis survival at high temperatures.
Collapse
|
17
|
Shaheen R, Mark P, Prevost CT, AlKindi A, Alhag A, Estwani F, Al-Sheddi T, Alobeid E, Alenazi MM, Ewida N, Ibrahim N, Hashem M, Abdulwahab F, Bryant EM, Spinelli E, Millichap J, Barnett SS, Kearney HM, Accogli A, Scala M, Capra V, Nigro V, Fu D, Alkuraya FS. Biallelic variants in CTU2 cause DREAM-PL syndrome and impair thiolation of tRNA wobble U34. Hum Mutat 2019; 40:2108-2120. [PMID: 31301155 DOI: 10.1002/humu.23870] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 07/07/2019] [Accepted: 07/08/2019] [Indexed: 01/29/2023]
Abstract
The wobble position in the anticodon loop of transfer ribonucleic acid (tRNA) is subject to numerous posttranscriptional modifications. In particular, thiolation of the wobble uridine has been shown to play an important role in codon-anticodon interactions. This modification is catalyzed by a highly conserved CTU1/CTU2 complex, disruption of which has been shown to cause abnormal phenotypes in yeast, worms, and plants. We have previously suggested that a single founder splicing variant in human CTU2 causes a novel multiple congenital anomalies syndrome consisting of dysmorphic facies, renal agenesis, ambiguous genitalia, microcephaly, polydactyly, and lissencephaly (DREAM-PL). In this study, we describe five new patients with DREAM-PL phenotype and whose molecular analysis expands the allelic heterogeneity of the syndrome to five different alleles; four of which predict protein truncation. Functional characterization using patient-derived cells for each of these alleles, as well as the original founder allele; revealed a specific impairment of wobble uridine thiolation in all known thiol-containing tRNAs. Our data establish a recognizable CTU2-linked autosomal recessive syndrome in humans characterized by defective thiolation of the wobble uridine. The potential deleterious consequences for the translational efficiency and fidelity during development as a mechanism for pathogenicity represent an attractive target of future investigations.
Collapse
Affiliation(s)
- Ranad Shaheen
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Saudi Arabia
| | - Paul Mark
- Spectrum Health Division of Medical Genetics, Grand Rapids, Michigan
| | - Christopher T Prevost
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, New York
| | - Adila AlKindi
- Genetics Department, Sultan Qaboos University Hospital, Muscat, Oman
| | - Ahmad Alhag
- Department of Pediatrics, Specialized Medical Center Hospital, Riyadh, Saudi Arabia
| | - Fatima Estwani
- Department of Pediatrics, Specialized Medical Center Hospital, Riyadh, Saudi Arabia
| | - Tarfa Al-Sheddi
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Saudi Arabia
| | - Eman Alobeid
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Saudi Arabia
| | - Mona M Alenazi
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Saudi Arabia
| | - Nour Ewida
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Saudi Arabia
| | - Niema Ibrahim
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Saudi Arabia
| | - Mais Hashem
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Saudi Arabia
| | - Firdous Abdulwahab
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Saudi Arabia
| | - Emily M Bryant
- Epilepsy Center and Division of Neurology, Ann & Robert H Lurie Children's Hospital of Chicago, Chicago, Illinois.,Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Egidio Spinelli
- Epilepsy Center and Division of Neurology, Ann & Robert H Lurie Children's Hospital of Chicago, Chicago, Illinois
| | - John Millichap
- Epilepsy Center and Division of Neurology, Ann & Robert H Lurie Children's Hospital of Chicago, Chicago, Illinois.,Department of Pediatrics and Neurology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Sarah S Barnett
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Hutton M Kearney
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Andrea Accogli
- Pediatric Neurology and Muscular Diseases Unit, Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, Istituto Giannina Gaslini, University of Genoa, Genoa, Italy
| | - Marcello Scala
- Department of Neurosurgery, IRCCS Istituto Giannina Gaslini, Genoa, Italy.,Pediatric Neurology and Muscular Diseases Unit, Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, Istituto Giannina Gaslini, University of Genoa, Genoa, Italy
| | - Valeria Capra
- Department of Neurosurgery, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Vincenzo Nigro
- Telethon Institute of Genetics and Medicine, Pozzuoli, Naples, Italy.,Department of Precision Medicine, University of Campania 'Luigi Vanvitelli', Naples, Italy
| | - Dragony Fu
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, New York
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Saudi Arabia.,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| |
Collapse
|
18
|
Mahanta N, Szantai-Kis DM, Petersson EJ, Mitchell DA. Biosynthesis and Chemical Applications of Thioamides. ACS Chem Biol 2019; 14:142-163. [PMID: 30698414 PMCID: PMC6404778 DOI: 10.1021/acschembio.8b01022] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Thioamidation as a posttranslational modification is exceptionally rare, with only a few reported natural products and exactly one known protein example (methyl-coenzyme M reductase from methane-metabolizing archaea). Recently, there has been significant progress in elucidating the biosynthesis and function of several thioamide-containing natural compounds. Separate developments in the chemical installation of thioamides into peptides and proteins have enabled cell biology and biophysical studies to advance the current understanding of natural thioamides. This review highlights the various strategies used by Nature to install thioamides in peptidic scaffolds and the potential functions of this rare but important modification. We also discuss synthetic methods used for the site-selective incorporation of thioamides into polypeptides with a brief discussion of the physicochemical implications. This account will serve as a foundation for the further study of thioamides in natural products and their various applications.
Collapse
Affiliation(s)
| | - D Miklos Szantai-Kis
- Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine , University of Pennsylvania , 3700 Hamilton Walk , Philadelphia , Pennsylvania 19104 , United States
| | - E James Petersson
- Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine , University of Pennsylvania , 3700 Hamilton Walk , Philadelphia , Pennsylvania 19104 , United States
- Department of Chemistry , University of Pennsylvania , 231 South 34th Street , Philadelphia , Pennsylvania 19104 , United States
| | | |
Collapse
|
19
|
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
|
20
|
Zhou G, Wang YS, Peng H, Huang XM, Xie XB, Shi QS. Role of Ttca of Citrobacter Werkmanii in Bacterial Growth, Biocides Resistance, Biofilm Formation and Swimming Motility. Int J Mol Sci 2018; 19:E2644. [PMID: 30200616 PMCID: PMC6165289 DOI: 10.3390/ijms19092644] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 08/28/2018] [Accepted: 08/30/2018] [Indexed: 01/10/2023] Open
Abstract
To screen, identify and study the genes involved in isothiazolone resistance and biofilm formation in Citrobacter werkmanii strain BF-6. A Tn5 transposon library of approximately 900 mutants of C. werkmanii strain BF-6 was generated and screened to isolate 1,2-benzisothiazolin-3-one (BIT) resistant strains. In addition, the tRNA 2-thiocytidine (32) synthetase gene (ttcA) was deleted through homologous recombination and the resulting phenotypic changes of the ΔttcA mutant were studied. A total of 3 genes were successfully identified, among which ΔttcA mutant exhibited a reduction in growth rate and swimming motility. On the other hand, an increase in biofilms formation in ΔttcA were observed but not with a significant resistance enhancement to BIT. This work, for the first time, highlights the role of ttcA gene of C. werkmanii strain BF-6 in BIT resistance and biofilm formation.
Collapse
Affiliation(s)
- Gang Zhou
- Guangdong Open Laboratory of Applied Microbiology, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangzhou, Guangdong 510070, China.
| | - Ying-Si Wang
- Guangdong Open Laboratory of Applied Microbiology, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangzhou, Guangdong 510070, China.
| | - Hong Peng
- Guangdong Open Laboratory of Applied Microbiology, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangzhou, Guangdong 510070, China.
| | - Xiao-Mo Huang
- Guangdong Open Laboratory of Applied Microbiology, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangzhou, Guangdong 510070, China.
| | - Xiao-Bao Xie
- Guangdong Open Laboratory of Applied Microbiology, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangzhou, Guangdong 510070, China.
| | - Qing-Shan Shi
- Guangdong Open Laboratory of Applied Microbiology, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangzhou, Guangdong 510070, China.
| |
Collapse
|
21
|
Romsang A, Duang-Nkern J, Khemsom K, Wongsaroj L, Saninjuk K, Fuangthong M, Vattanaviboon P, Mongkolsuk S. Pseudomonas aeruginosa ttcA encoding tRNA-thiolating protein requires an iron-sulfur cluster to participate in hydrogen peroxide-mediated stress protection and pathogenicity. Sci Rep 2018; 8:11882. [PMID: 30089777 PMCID: PMC6082896 DOI: 10.1038/s41598-018-30368-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 07/27/2018] [Indexed: 01/21/2023] Open
Abstract
During the translation process, transfer RNA (tRNA) carries amino acids to ribosomes for protein synthesis. Each codon of mRNA is recognized by a specific tRNA, and enzyme-catalysed modifications to tRNA regulate translation. TtcA is a unique tRNA-thiolating enzyme that requires an iron-sulfur ([Fe-S]) cluster to catalyse thiolation of tRNA. In this study, the physiological functions of a putative ttcA in Pseudomonas aeruginosa, an opportunistic human pathogen that causes serious problems in hospitals, were characterized. A P. aeruginosa ttcA-deleted mutant was constructed, and mutant cells were rendered hypersensitive to oxidative stress, such as hydrogen peroxide (H2O2) treatment. Catalase activity was lower in the ttcA mutant, suggesting that this gene plays a role in protecting against oxidative stress. Moreover, the ttcA mutant demonstrated attenuated virulence in a Drosophila melanogaster host model. Site-directed mutagenesis analysis revealed that the conserved cysteine motifs involved in [Fe-S] cluster ligation were required for TtcA function. Furthermore, ttcA expression increased upon H2O2 exposure, implying that enzyme levels are induced under stress conditions. Overall, the data suggest that P. aeruginosa ttcA plays a critical role in protecting against oxidative stress via catalase activity and is required for successful bacterial infection of the host.
Collapse
Affiliation(s)
- Adisak Romsang
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand. .,Center for Emerging Bacterial Infections, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.
| | - Jintana Duang-Nkern
- Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | - Khwannarin Khemsom
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Lampet Wongsaroj
- Molecular Medicine Graduate Program, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Kritsakorn Saninjuk
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Mayuree Fuangthong
- Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | - Paiboon Vattanaviboon
- Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | - Skorn Mongkolsuk
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.,Center for Emerging Bacterial Infections, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.,Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, 10210, Thailand.,Molecular Medicine Graduate Program, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| |
Collapse
|
22
|
Aučynaitė A, Rutkienė R, Gasparavičiūtė R, Meškys R, Urbonavičius J. A gene encoding a DUF523 domain protein is involved in the conversion of 2-thiouracil into uracil. ENVIRONMENTAL MICROBIOLOGY REPORTS 2018; 10:49-56. [PMID: 29194984 DOI: 10.1111/1758-2229.12605] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 11/17/2017] [Accepted: 11/19/2017] [Indexed: 06/07/2023]
Abstract
Modified nucleotides are present in many RNA species in all Domains of Life. While the biosynthetic pathways of such nucleotides are well studied, much less is known about the degradation of RNAs and the return to the metabolism of modified nucleotides, their respective nucleosides or heterocyclic bases. Using an E. coli uracil auxotroph, we screened the metagenomic libraries for genes, which would allow the conversion of 2-thiouracil to uracil and thereby lead to the growth on a defined synthetic medium. We show that a gene encoding a protein consisting of previously uncharacterized Domain of Unknown Function 523 (DUF523) is responsible for such phenotype. We have purified this recombinant protein and demonstrated that it contains a FeS cluster. The substitution of cysteines, which have been predicted to form such clusters, with alanines abolished the growth phenotype. We conclude that DUF523 is involved in the conversion of 2-thiouracil into uracil in vivo.
Collapse
Affiliation(s)
- Agota Aučynaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Rasa Rutkienė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Renata Gasparavičiūtė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Jaunius Urbonavičius
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
- Department of Chemistry and Bioengineering, Vilnius Gediminas Technical University, Vilnius, Lithuania
| |
Collapse
|
23
|
Agris PF, Eruysal ER, Narendran A, Väre VYP, Vangaveti S, Ranganathan SV. Celebrating wobble decoding: Half a century and still much is new. RNA Biol 2017; 15:537-553. [PMID: 28812932 PMCID: PMC6103715 DOI: 10.1080/15476286.2017.1356562] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 07/04/2017] [Accepted: 07/06/2017] [Indexed: 10/25/2022] Open
Abstract
A simple post-transcriptional modification of tRNA, deamination of adenosine to inosine at the first, or wobble, position of the anticodon, inspired Francis Crick's Wobble Hypothesis 50 years ago. Many more naturally-occurring modifications have been elucidated and continue to be discovered. The post-transcriptional modifications of tRNA's anticodon domain are the most diverse and chemically complex of any RNA modifications. Their contribution with regards to chemistry, structure and dynamics reveal individual and combined effects on tRNA function in recognition of cognate and wobble codons. As forecast by the Modified Wobble Hypothesis 25 years ago, some individual modifications at tRNA's wobble position have evolved to restrict codon recognition whereas others expand the tRNA's ability to read as many as four synonymous codons. Here, we review tRNA wobble codon recognition using specific examples of simple and complex modification chemistries that alter tRNA function. Understanding natural modifications has inspired evolutionary insights and possible innovation in protein synthesis.
Collapse
Affiliation(s)
- Paul F. Agris
- The RNA Institute, State University of New York, Albany, NY, USA
- Department of Biology, State University of New York, Albany, NY, USA
- Department of Chemistry, State University of New York, Albany, NY, USA
| | - Emily R. Eruysal
- Department of Biology, State University of New York, Albany, NY, USA
| | - Amithi Narendran
- Department of Biology, State University of New York, Albany, NY, USA
| | - Ville Y. P. Väre
- Department of Biology, State University of New York, Albany, NY, USA
| | - Sweta Vangaveti
- The RNA Institute, State University of New York, Albany, NY, USA
| | | |
Collapse
|
24
|
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
|
25
|
Agris PF, Narendran A, Sarachan K, Väre VYP, Eruysal E. The Importance of Being Modified: The Role of RNA Modifications in Translational Fidelity. Enzymes 2017; 41:1-50. [PMID: 28601219 DOI: 10.1016/bs.enz.2017.03.005] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The posttranscriptional modifications of tRNA's anticodon stem and loop (ASL) domain represent a third level, a third code, to the accuracy and efficiency of translating mRNA codons into the correct amino acid sequence of proteins. Modifications of tRNA's ASL domain are enzymatically synthesized and site specifically located at the anticodon wobble position-34 and 3'-adjacent to the anticodon at position-37. Degeneracy of the 64 Universal Genetic Codes and the limitation in the number of tRNA species require some tRNAs to decode more than one codon. The specific modification chemistries and their impact on the tRNA's ASL structure and dynamics enable one tRNA to decode cognate and "wobble codons" or to expand recognition to synonymous codons, all the while maintaining the translational reading frame. Some modified nucleosides' chemistries prestructure tRNA to read the two codons of a specific amino acid that shares a twofold degenerate codon box, and other chemistries allow a different tRNA to respond to all four codons of a fourfold degenerate codon box. Thus, tRNA ASL modifications are critical and mutations in genes for the modification enzymes and tRNA, the consequences of which is a lack of modification, lead to mistranslation and human disease. By optimizing tRNA anticodon chemistries, structure, and dynamics in all organisms, modifications ensure translational fidelity of mRNA transcripts.
Collapse
Affiliation(s)
- Paul F Agris
- The RNA Institute, State University of New York, Albany, NY, United States.
| | - Amithi Narendran
- The RNA Institute, State University of New York, Albany, NY, United States
| | - Kathryn Sarachan
- The RNA Institute, State University of New York, Albany, NY, United States
| | - Ville Y P Väre
- The RNA Institute, State University of New York, Albany, NY, United States
| | - Emily Eruysal
- The RNA Institute, State University of New York, Albany, NY, United States
| |
Collapse
|
26
|
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
|
27
|
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: 48] [Impact Index Per Article: 6.9] [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
|
28
|
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
|
29
|
Iñigo S, Durand AN, Ritter A, Le Gall S, Termathe M, Klassen R, Tohge T, De Coninck B, Van Leene J, De Clercq R, Cammue BPA, Fernie AR, Gevaert K, De Jaeger G, Leidel SA, Schaffrath R, Van Lijsebettens M, Pauwels L, Goossens A. Glutaredoxin GRXS17 Associates with the Cytosolic Iron-Sulfur Cluster Assembly Pathway. PLANT PHYSIOLOGY 2016; 172:858-873. [PMID: 27503603 PMCID: PMC5047072 DOI: 10.1104/pp.16.00261] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 08/03/2016] [Indexed: 05/12/2023]
Abstract
Cytosolic monothiol glutaredoxins (GRXs) are required in iron-sulfur (Fe-S) cluster delivery and iron sensing in yeast and mammals. In plants, it is unclear whether they have similar functions. Arabidopsis (Arabidopsis thaliana) has a sole class II cytosolic monothiol GRX encoded by GRXS17 Here, we used tandem affinity purification to establish that Arabidopsis GRXS17 associates with most known cytosolic Fe-S assembly (CIA) components. Similar to mutant plants with defective CIA components, grxs17 loss-of-function mutants showed some degree of hypersensitivity to DNA damage and elevated expression of DNA damage marker genes. We also found that several putative Fe-S client proteins directly bind to GRXS17, such as XANTHINE DEHYDROGENASE1 (XDH1), involved in the purine salvage pathway, and CYTOSOLIC THIOURIDYLASE SUBUNIT1 and CYTOSOLIC THIOURIDYLASE SUBUNIT2, both essential for the 2-thiolation step of 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U) modification of tRNAs. Correspondingly, profiling of the grxs17-1 mutant pointed to a perturbed flux through the purine degradation pathway and revealed that it phenocopied mutants in the elongator subunit ELO3, essential for the mcm5 tRNA modification step, although we did not find XDH1 activity or tRNA thiolation to be markedly reduced in the grxs17-1 mutant. Taken together, our data suggest that plant cytosolic monothiol GRXs associate with the CIA complex, as in other eukaryotes, and contribute to, but are not essential for, the correct functioning of client Fe-S proteins in unchallenged conditions.
Collapse
Affiliation(s)
- Sabrina Iñigo
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Astrid Nagels Durand
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Andrés Ritter
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Sabine Le Gall
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Martin Termathe
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Roland Klassen
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Takayuki Tohge
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Barbara De Coninck
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Jelle Van Leene
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Rebecca De Clercq
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Bruno P A Cammue
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Alisdair R Fernie
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Kris Gevaert
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Geert De Jaeger
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Sebastian A Leidel
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Raffael Schaffrath
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Mieke Van Lijsebettens
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Laurens Pauwels
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Alain Goossens
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| |
Collapse
|
30
|
Jaroensuk J, Atichartpongkul S, Chionh YH, Wong YH, Liew CW, McBee ME, Thongdee N, Prestwich EG, DeMott MS, Mongkolsuk S, Dedon PC, Lescar J, Fuangthong M. Methylation at position 32 of tRNA catalyzed by TrmJ alters oxidative stress response in Pseudomonas aeruginosa. Nucleic Acids Res 2016; 44:10834-10848. [PMID: 27683218 PMCID: PMC5159551 DOI: 10.1093/nar/gkw870] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 09/17/2016] [Accepted: 09/20/2016] [Indexed: 02/04/2023] Open
Abstract
Bacteria respond to environmental stresses using a variety of signaling and gene expression pathways, with translational mechanisms being the least well understood. Here, we identified a tRNA methyltransferase in Pseudomonas aeruginosa PA14, trmJ, which confers resistance to oxidative stress. Analysis of tRNA from a trmJ mutant revealed that TrmJ catalyzes formation of Cm, Um, and, unexpectedly, Am. Defined in vitro analyses revealed that tRNAMet(CAU) and tRNATrp(CCA) are substrates for Cm formation, tRNAGln(UUG), tRNAPro(UGG), tRNAPro(CGG) and tRNAHis(GUG) for Um, and tRNAPro(GGG) for Am. tRNASer(UGA), previously observed as a TrmJ substrate in Escherichia coli, was not modified by PA14 TrmJ. Position 32 was confirmed as the TrmJ target for Am in tRNAPro(GGG) and Um in tRNAGln(UUG) by mass spectrometric analysis. Crystal structures of the free catalytic N-terminal domain of TrmJ show a 2-fold symmetrical dimer with an active site located at the interface between the monomers and a flexible basic loop positioned to bind tRNA, with conformational changes upon binding of the SAM-analog sinefungin. The loss of TrmJ rendered PA14 sensitive to H2O2 exposure, with reduced expression of oxyR-recG, katB-ankB, and katE. These results reveal that TrmJ is a tRNA:Cm32/Um32/Am32 methyltransferase involved in translational fidelity and the oxidative stress response.
Collapse
Affiliation(s)
- Juthamas Jaroensuk
- Applied Biological Sciences Program, Chulabhorn Graduate Institute, Bangkok, Thailand.,Singapore-MIT Alliance for Research and Technology, Singapore
| | | | - Yok Hian Chionh
- Singapore-MIT Alliance for Research and Technology, Singapore
| | - Yee Hwa Wong
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Chong Wai Liew
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore
| | - Megan E McBee
- Singapore-MIT Alliance for Research and Technology, Singapore
| | - Narumon Thongdee
- Applied Biological Sciences Program, Chulabhorn Graduate Institute, Bangkok, Thailand
| | - Erin G Prestwich
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Michael S DeMott
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Skorn Mongkolsuk
- Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand.,Department of Biotechnology, Faculty of Sciences, Mahidol University, Bangkok, Thailand.,Center of Excellence on Environmental Health and Toxicology (EHT), Bangkok, Thailand
| | - Peter C Dedon
- Singapore-MIT Alliance for Research and Technology, Singapore .,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Julien Lescar
- School of Biological Sciences, Nanyang Technological University, Singapore .,NTU Institute of Structural Biology, Nanyang Technological University, Singapore.,UPMC UMRS CR7 - CNRS ERL 8255-INSERM U1135 Centre d' Immunologie et des Maladies Infectieuses, Paris, France
| | - Mayuree Fuangthong
- Applied Biological Sciences Program, Chulabhorn Graduate Institute, Bangkok, Thailand .,Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand.,Center of Excellence on Environmental Health and Toxicology (EHT), Bangkok, Thailand
| |
Collapse
|
31
|
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]
|
32
|
Abstract
Transfer RNA (tRNA) from all organisms on this planet contains modified nucleosides, which are derivatives of the four major nucleosides. tRNA from Escherichia coli/Salmonella enterica contains 31 different modified nucleosides, which are all, except for one (Queuosine[Q]), synthesized on an oligonucleotide precursor, which through specific enzymes later matures into tRNA. The corresponding structural genes for these enzymes are found in mono- and polycistronic operons, the latter of which have a complex transcription and translation pattern. The syntheses of some of them (e.g.,several methylated derivatives) are catalyzed by one enzyme, which is position and base specific, but synthesis of some have a very complex biosynthetic pathway involving several enzymes (e.g., 2-thiouridines, N6-threonyladenosine [t6A],and Q). Several of the modified nucleosides are essential for viability (e.g.,lysidin, t6A, 1-methylguanosine), whereas deficiency in others induces severe growth defects. However, some have no or only a small effect on growth at laboratory conditions. Modified nucleosides that are present in the anticodon loop or stem have a fundamental influence on the efficiency of charging the tRNA, reading cognate codons, and preventing missense and frameshift errors. Those, which are present in the body of the tRNA, have a primarily stabilizing effect on the tRNA. Thus, the ubiquitouspresence of these modified nucleosides plays a pivotal role in the function of the tRNA by their influence on the stability and activity of the tRNA.
Collapse
|
33
|
Iron-sulfur proteins responsible for RNA modifications. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1853:1272-83. [PMID: 25533083 DOI: 10.1016/j.bbamcr.2014.12.010] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 12/08/2014] [Accepted: 12/09/2014] [Indexed: 12/22/2022]
Abstract
RNA molecules are decorated with various chemical modifications, which are introduced post-transcriptionally by RNA-modifying enzymes. These modifications are required for proper RNA function. Among more than 100 known species of RNA modifications, several modified bases in tRNAs and rRNAs are introduced by RNA-modifying enzymes containing iron-sulfur (Fe/S) clusters. Most Fe/S-containing RNA-modifying enzymes contain radical SAM domains that catalyze a variety of chemical reactions, including methylation, methylthiolation, carboxymethylation, tricyclic purine formation, and deazaguanine formation. Lack of these modifications can cause pathological consequences. Here, we review recent studies on the biogenesis and function of RNA modifications mediated by Fe/S proteins. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.
Collapse
|
34
|
Bouvier D, Labessan N, Clémancey M, Latour JM, Ravanat JL, Fontecave M, Atta M. TtcA a new tRNA-thioltransferase with an Fe-S cluster. Nucleic Acids Res 2014; 42:7960-70. [PMID: 24914049 PMCID: PMC4081106 DOI: 10.1093/nar/gku508] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
TtcA catalyzes the post-transcriptional thiolation of cytosine 32 in some tRNAs. The enzyme from Escherichia coli was homologously overexpressed in E. coli. The purified enzyme is a dimer containing an iron-sulfur cluster and displays activity in in vitro assays. The type and properties of the cluster were investigated using a combination of UV-visible absorption, EPR and Mössbauer spectroscopy, as well as by site-directed mutagenesis. These studies demonstrated that the TtcA enzyme contains a redox-active and oxygen-sensitive [4Fe-4S] cluster, chelated by only three cysteine residues and absolutely essential for activity. TtcA is unique tRNA-thiolating enzyme using an iron-sulfur cluster for catalyzing a non-redox reaction.
Collapse
Affiliation(s)
- Denis Bouvier
- University of Grenoble Alpes, iRTSV-LCBM, UMR5249, F-38000 Grenoble, France CNRS, iRTSV-LCBM, UMR5249, F-38000 Grenoble, France CEA, iRTSV-LCBM, UMR5249, F-38000 Grenoble, France
| | - Natty Labessan
- University of Grenoble Alpes, iRTSV-LCBM, UMR5249, F-38000 Grenoble, France CNRS, iRTSV-LCBM, UMR5249, F-38000 Grenoble, France CEA, iRTSV-LCBM, UMR5249, F-38000 Grenoble, France
| | - Martin Clémancey
- University of Grenoble Alpes, iRTSV-LCBM, UMR5249, F-38000 Grenoble, France CNRS, iRTSV-LCBM, UMR5249, F-38000 Grenoble, France CEA, iRTSV-LCBM, UMR5249, F-38000 Grenoble, France
| | - Jean-Marc Latour
- University of Grenoble Alpes, iRTSV-LCBM, UMR5249, F-38000 Grenoble, France CNRS, iRTSV-LCBM, UMR5249, F-38000 Grenoble, France CEA, iRTSV-LCBM, UMR5249, F-38000 Grenoble, France
| | - Jean-Luc Ravanat
- University of Grenoble Alpes, INAC, SCIB, F-38000 Grenoble, France CEA, iNAC, SCIB, F-38054 Grenoble, France
| | - Marc Fontecave
- University of Grenoble Alpes, iRTSV-LCBM, UMR5249, F-38000 Grenoble, France CNRS, iRTSV-LCBM, UMR5249, F-38000 Grenoble, France CEA, iRTSV-LCBM, UMR5249, F-38000 Grenoble, France Laboratoire de Chimie des Processus Biologiques, UMR 8229 Collège de France/CNRS/UPMC, 11 place Marcellin-Berthelot, Paris, France
| | - Mohamed Atta
- University of Grenoble Alpes, iRTSV-LCBM, UMR5249, F-38000 Grenoble, France CNRS, iRTSV-LCBM, UMR5249, F-38000 Grenoble, France CEA, iRTSV-LCBM, UMR5249, F-38000 Grenoble, France
| |
Collapse
|
35
|
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
|
36
|
Björk GR, Hagervall TG. Transfer RNA Modification: Presence, Synthesis, and Function. EcoSal Plus 2014; 6. [PMID: 26442937 DOI: 10.1128/ecosalplus.esp-0007-2013] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Indexed: 06/05/2023]
Abstract
Transfer RNA (tRNA) from all organisms on this planet contains modified nucleosides, which are derivatives of the four major nucleosides. tRNA from Escherichia coli/Salmonella enterica serovar Typhimurium contains 33 different modified nucleosides, which are all, except one (Queuosine [Q]), synthesized on an oligonucleotide precursor, which by specific enzymes later matures into tRNA. The structural genes for these enzymes are found in mono- and polycistronic operons, the latter of which have a complex transcription and translation pattern. The synthesis of the tRNA-modifying enzymes is not regulated similarly, and it is not coordinated to that of their substrate, the tRNA. The synthesis of some of them (e.g., several methylated derivatives) is catalyzed by one enzyme, which is position and base specific, whereas synthesis of some has a very complex biosynthetic pathway involving several enzymes (e.g., 2-thiouridines, N 6-cyclicthreonyladenosine [ct6A], and Q). Several of the modified nucleosides are essential for viability (e.g., lysidin, ct6A, 1-methylguanosine), whereas the deficiency of others induces severe growth defects. However, some have no or only a small effect on growth at laboratory conditions. Modified nucleosides that are present in the anticodon loop or stem have a fundamental influence on the efficiency of charging the tRNA, reading cognate codons, and preventing missense and frameshift errors. Those that are present in the body of the tRNA primarily have a stabilizing effect on the tRNA. Thus, the ubiquitous presence of these modified nucleosides plays a pivotal role in the function of the tRNA by their influence on the stability and activity of the tRNA.
Collapse
Affiliation(s)
- Glenn R Björk
- Department of Molecular Biology, Umeå University, S-90187 Umeå, Sweden
| | - Tord G Hagervall
- Department of Molecular Biology, Umeå University, S-90187 Umeå, Sweden
| |
Collapse
|
37
|
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: 63] [Impact Index Per Article: 6.3] [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
|
38
|
Liu Y, Long F, Wang L, Söll D, Whitman WB. The putative tRNA 2-thiouridine synthetase Ncs6 is an essential sulfur carrier in Methanococcus maripaludis. FEBS Lett 2014; 588:873-7. [PMID: 24530533 DOI: 10.1016/j.febslet.2014.01.065] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Revised: 01/28/2014] [Accepted: 01/29/2014] [Indexed: 11/16/2022]
Abstract
Thiolation of carbon-2 of uridine located in the first position of the anticodons of tRNAUUG(Gln), tRNAUUC(Glu), and tRNAUUU(Lys) is a conserved RNA modification event requiring the 2-thiouridine synthetase Ncs6/Ctu1 in archaea and eukaryotes. Ncs6/Ctu1 activates uridine by adenylation, but its role in sulfur transfer is unclear. Here we show that Mmp1356, the Ncs6/Ctu1 homolog in the archaeon Methanococcus maripaludis, forms a persulfide enzyme adduct with an active site cysteine; this suggests that Mmp1356 directly participates in sulfur transfer as a persulfide carrier. Transposon mutagenesis shows that Mmp1356 is likely to be an essential protein.
Collapse
Affiliation(s)
- Yuchen Liu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA.
| | - Feng Long
- Department of Microbiology, University of Georgia, Athens, GA 30602-2605, USA
| | - Liangliang Wang
- Department of Microbiology, University of Georgia, Athens, GA 30602-2605, USA
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA; Department of Chemistry, Yale University, New Haven, CT 06520-8114, USA
| | - William B Whitman
- Department of Microbiology, University of Georgia, Athens, GA 30602-2605, USA
| |
Collapse
|
39
|
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
|
40
|
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
|
41
|
Cantara WA, Bilbille Y, Kim J, Kaiser R, Leszczyńska G, Malkiewicz A, Agris PF. Modifications Modulate Anticodon Loop Dynamics and Codon Recognition of E. coli tRNAArg1,2. J Mol Biol 2012; 416:579-97. [DOI: 10.1016/j.jmb.2011.12.054] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2011] [Revised: 12/13/2011] [Accepted: 12/27/2011] [Indexed: 10/14/2022]
|
42
|
Maynard ND, Macklin DN, Kirkegaard K, Covert MW. Competing pathways control host resistance to virus via tRNA modification and programmed ribosomal frameshifting. Mol Syst Biol 2012; 8:567. [PMID: 22294093 PMCID: PMC3296357 DOI: 10.1038/msb.2011.101] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Accepted: 12/14/2011] [Indexed: 11/25/2022] Open
Abstract
Viral infection depends on a complex interplay between host and viral factors. Here, we link host susceptibility to viral infection to a network encompassing sulfur metabolism, tRNA modification, competitive binding, and programmed ribosomal frameshifting (PRF). We first demonstrate that the iron-sulfur cluster biosynthesis pathway in Escherichia coli exerts a protective effect during lambda phage infection, while a tRNA thiolation pathway enhances viral infection. We show that tRNA(Lys) uridine 34 modification inhibits PRF to influence the ratio of lambda phage proteins gpG and gpGT. Computational modeling and experiments suggest that the role of the iron-sulfur cluster biosynthesis pathway in infection is indirect, via competitive binding of the shared sulfur donor IscS. Based on the universality of many key components of this network, in both the host and the virus, we anticipate that these findings may have broad relevance to understanding other infections, including viral infection of humans.
Collapse
Affiliation(s)
| | - Derek N Macklin
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Karla Kirkegaard
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Markus W Covert
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| |
Collapse
|
43
|
E1- and ubiquitin-like proteins provide a direct link between protein conjugation and sulfur transfer in archaea. Proc Natl Acad Sci U S A 2011; 108:4417-22. [PMID: 21368171 DOI: 10.1073/pnas.1018151108] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Based on our recent work with Haloferax volcanii, ubiquitin-like (Ubl) proteins (SAMP1 and SAMP2) are known to be covalently attached to proteins in archaea. Here, we investigated the enzymes required for the formation of these Ubl-protein conjugates (SAMPylation) and whether this system is linked to sulfur transfer. Markerless in-frame deletions were generated in H. volcanii target genes. The mutants were examined for: (i) the formation of Ubl protein conjugates, (ii) growth under various conditions, including those requiring the synthesis of the sulfur-containing molybdenum cofactor (MoCo), and (iii) the thiolation of tRNA. With this approach we found that UbaA of the E1/MoeB/ThiF superfamily was required for the formation of both SAMP1- and SAMP2-protein conjugates. In addition, UbaA, SAMP1, and MoaE (a homolog of the large subunit of molybdopterin synthase) were essential for MoCo-dependent dimethyl sulfoxide reductase activity, suggesting that these proteins function in MoCo-biosynthesis. UbaA and SAMP2 were also crucial for optimal growth at high temperature and the thiolation of tRNA. Based on these results, we propose a working model for archaea in which the E1-like UbaA can activate multiple Ubl SAMPs for protein conjugation as well as for sulfur transfer. In sulfur transfer, SAMP1 and SAMP2 appear specific for MoCo biosynthesis and the thiolation of tRNA, respectively. Overall, this study provides a fundamental insight into the diverse cellular functions of the Ubl system.
Collapse
|
44
|
Benítez-Páez A, Villarroya M, Douthwaite S, Gabaldón T, Armengod ME. YibK is the 2'-O-methyltransferase TrmL that modifies the wobble nucleotide in Escherichia coli tRNA(Leu) isoacceptors. RNA (NEW YORK, N.Y.) 2010; 16:2131-43. [PMID: 20855540 PMCID: PMC2957053 DOI: 10.1261/rna.2245910] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2010] [Accepted: 08/18/2010] [Indexed: 05/25/2023]
Abstract
Transfer RNAs are the most densely modified nucleic acid molecules in living cells. In Escherichia coli, more than 30 nucleoside modifications have been characterized, ranging from methylations and pseudouridylations to more complex additions that require multiple enzymatic steps. Most of the modifying enzymes have been identified, although a few notable exceptions include the 2'-O-methyltransferase(s) that methylate the ribose at the nucleotide 34 wobble position in the two leucyl isoacceptors tRNA(Leu)(CmAA) and tRNA(Leu)(cmnm5UmAA). Here, we have used a comparative genomics approach to uncover candidate E. coli genes for the missing enzyme(s). Transfer RNAs from null mutants for candidate genes were analyzed by mass spectrometry and revealed that inactivation of yibK leads to loss of 2'-O-methylation at position 34 in both tRNA(Leu)(CmAA) and tRNA(Leu)(cmnm5UmAA). Loss of YibK methylation reduces the efficiency of codon-wobble base interaction, as demonstrated in an amber suppressor supP system. Inactivation of yibK had no detectable effect on steady-state growth rate, although a distinct disadvantage was noted in multiple-round, mixed-population growth experiments, suggesting that the ability to recover from the stationary phase was impaired. Methylation is restored in vivo by complementing with a recombinant copy of yibK. Despite being one of the smallest characterized α/β knot proteins, YibK independently catalyzes the methyl transfer from S-adenosyl-L-methionine to the 2'-OH of the wobble nucleotide; YibK recognition of this target requires a pyridine at position 34 and N⁶-(isopentenyl)-2-methylthioadenosine at position 37. YibK is one of the last remaining E. coli tRNA modification enzymes to be identified and is now renamed TrmL.
Collapse
Affiliation(s)
- Alfonso Benítez-Páez
- Laboratorio de Genética Molecular, Centro de Investigación Príncipe Felipe, 46012 Valencia, Spain
| | | | | | | | | |
Collapse
|
45
|
Han GW, Yang XL, McMullan D, Chong YE, Krishna SS, Rife CL, Weekes D, Brittain SM, Abdubek P, Ambing E, Astakhova T, Axelrod HL, Carlton D, Caruthers J, Chiu HJ, Clayton T, Duan L, Feuerhelm J, Grant JC, Grzechnik SK, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kumar A, Marciano D, Miller MD, Morse AT, Nigoghossian E, Okach L, Paulsen J, Reyes R, van den Bedem H, White A, Wolf G, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Elsliger MA, Schimmel P, Wilson IA. Structure of a tryptophanyl-tRNA synthetase containing an iron-sulfur cluster. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:1326-34. [PMID: 20944229 PMCID: PMC2954223 DOI: 10.1107/s1744309110037619] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Accepted: 09/20/2010] [Indexed: 11/10/2022]
Abstract
A novel aminoacyl-tRNA synthetase that contains an iron-sulfur cluster in the tRNA anticodon-binding region and efficiently charges tRNA with tryptophan has been found in Thermotoga maritima. The crystal structure of TmTrpRS (tryptophanyl-tRNA synthetase; TrpRS; EC 6.1.1.2) reveals an iron-sulfur [4Fe-4S] cluster bound to the tRNA anticodon-binding (TAB) domain and an L-tryptophan ligand in the active site. None of the other T. maritima aminoacyl-tRNA synthetases (AARSs) contain this [4Fe-4S] cluster-binding motif (C-x₂₂-C-x₆-C-x₂-C). It is speculated that the iron-sulfur cluster contributes to the stability of TmTrpRS and could play a role in the recognition of the anticodon.
Collapse
Affiliation(s)
- Gye Won Han
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Xiang-Lei Yang
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Daniel McMullan
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Yeeting E. Chong
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - S. Sri Krishna
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - Christopher L. Rife
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Dana Weekes
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - Scott M. Brittain
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Polat Abdubek
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Eileen Ambing
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Tamara Astakhova
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Herbert L. Axelrod
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Dennis Carlton
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Jonathan Caruthers
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Hsiu-Ju Chiu
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Thomas Clayton
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Lian Duan
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Julie Feuerhelm
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Joanna C. Grant
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Slawomir K. Grzechnik
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Lukasz Jaroszewski
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - Kevin K. Jin
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Heath E. Klock
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Mark W. Knuth
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Abhinav Kumar
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - David Marciano
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Mitchell D. Miller
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Andrew T. Morse
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Edward Nigoghossian
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Linda Okach
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Jessica Paulsen
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Ron Reyes
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Henry van den Bedem
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Aprilfawn White
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Guenter Wolf
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Qingping Xu
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Keith O. Hodgson
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Photon Science, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - John Wooley
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Ashley M. Deacon
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Adam Godzik
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - Scott A. Lesley
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Marc-André Elsliger
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Paul Schimmel
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ian A. Wilson
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| |
Collapse
|
46
|
Shi R, Proteau A, Villarroya M, Moukadiri I, Zhang L, Trempe JF, Matte A, Armengod ME, Cygler M. Structural basis for Fe-S cluster assembly and tRNA thiolation mediated by IscS protein-protein interactions. PLoS Biol 2010; 8:e1000354. [PMID: 20404999 PMCID: PMC2854127 DOI: 10.1371/journal.pbio.1000354] [Citation(s) in RCA: 205] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2009] [Accepted: 03/08/2010] [Indexed: 11/30/2022] Open
Abstract
Crystal structures reveal how distinct sites on the cysteine desulfurase IscS bind two different sulfur-acceptor proteins, IscU and TusA, to transfer sulfur atoms for iron-sulfur cluster biosynthesis and tRNA thiolation. The cysteine desulfurase IscS is a highly conserved master enzyme initiating sulfur transfer via persulfide to a range of acceptor proteins involved in Fe-S cluster assembly, tRNA modifications, and sulfur-containing cofactor biosynthesis. Several IscS-interacting partners including IscU, a scaffold for Fe-S cluster assembly; TusA, the first member of a sulfur relay leading to sulfur incorporation into the wobble uridine of several tRNAs; ThiI, involved in tRNA modification and thiamine biosynthesis; and rhodanese RhdA are sulfur acceptors. Other proteins, such as CyaY/frataxin and IscX, also bind to IscS, but their functional roles are not directly related to sulfur transfer. We have determined the crystal structures of IscS-IscU and IscS-TusA complexes providing the first insight into their different modes of binding and the mechanism of sulfur transfer. Exhaustive mutational analysis of the IscS surface allowed us to map the binding sites of various partner proteins and to determine the functional and biochemical role of selected IscS and TusA residues. IscS interacts with its partners through an extensive surface area centered on the active site Cys328. The structures indicate that the acceptor proteins approach Cys328 from different directions and suggest that the conformational plasticity of a long loop containing this cysteine is essential for the ability of IscS to transfer sulfur to multiple acceptor proteins. The sulfur acceptors can only bind to IscS one at a time, while frataxin and IscX can form a ternary complex with IscU and IscS. Our data support the role of frataxin as an iron donor for IscU to form the Fe-S clusters. Sulfur is incorporated into the backbone of almost all proteins in the form of the amino acids cysteine and methionine. In some proteins, sulfur is also present as iron–sulfur clusters, sulfur-containing vitamins, and cofactors. What's more, sulfur is important in the structure of tRNAs, which are crucial for translation of the genetic code from messenger RNA for protein synthesis. The biosynthetic pathways for assembly of these sulfur-containing molecules are generally well known, but the molecular details of how sulfur is delivered from protein to protein are less well understood. In bacteria, one of three pathways for sulfur delivery is the isc (iron-sulfur clusters) system. First, an enzyme called IscS extracts sulfur atoms from cysteine. This versatile enzyme can then interact with several proteins to deliver sulfur to various pathways that make iron–sulfur clusters or transfer sulfur to cofactors and tRNAs. This study describes in atomic detail precisely how IscS binds in a specific and yet distinct way to two different proteins: IscU (a scaffold protein for iron–sulfur cluster formation) and TusA (which delivers sulfur for tRNA modification). Furthermore, by introducing mutations into IscS, we have identified the region on the surface of this protein that is involved in binding its target proteins. These findings provide a molecular view of the protein–protein interactions involved in sulfur transfer and advance our understanding of how sulfur is delivered from one protein to another during biosynthesis of iron–sulfur clusters.
Collapse
Affiliation(s)
- Rong Shi
- Department of Biochemistry, McGill University, Montréal, Québec, Canada
| | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Spontaneous excision of the Salmonella enterica serovar Enteritidis-specific defective prophage-like element phiSE14. J Bacteriol 2010; 192:2246-54. [PMID: 20172996 DOI: 10.1128/jb.00270-09] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Salmonella enterica serovar Enteritidis has emerged as a major health problem worldwide in the last few decades. DNA loci unique to S. Enteritidis can provide markers for detection of this pathogen and may reveal pathogenic mechanisms restricted to this serovar. An in silico comparison of 16 Salmonella genomic sequences revealed the presence of an approximately 12.5-kb genomic island (GEI) specific to the sequenced S. Enteritidis strain NCTC13349. The GEI is inserted at the 5' end of gene ydaO (SEN1377), is flanked by 308-bp imperfect direct repeats (attL and attR), and includes 21 open reading frames (SEN1378 to SEN1398), encoding primarily phage-related proteins. Accordingly, this GEI has been annotated as the defective prophage SE14 in the genome of strain NCTC13349. The genetic structure and location of phiSE14 are conserved in 99 of 103 wild-type strains of S. Enteritidis studied here, including reference strains NCTC13349 and LK5. Notably, an extrachromosomal circular form of phiSE14 was detected in every strain carrying this island. The presence of attP sites in the circular forms detected in NCTC13349 and LK5 was confirmed. In addition, we observed spontaneous loss of a tetRA-tagged version of phiSE14, leaving an empty attB site in the genome of strain NCTC13349. Collectively, these results demonstrate that phiSE14 is an unstable genetic element that undergoes spontaneous excision under standard growth conditions. An internal fragment of phiSE14 designated Sdf I has been used as a serovar-specific genetic marker in PCR-based detection systems and as a tool to determine S. Enteritidis levels in experimental infections. The instability of this region may require a reassessment of its suitability for such applications.
Collapse
|
48
|
Grosjean H, de Crécy-Lagard V, Marck C. Deciphering synonymous codons in the three domains of life: co-evolution with specific tRNA modification enzymes. FEBS Lett 2010; 584:252-64. [PMID: 19931533 DOI: 10.1016/j.febslet.2009.11.052] [Citation(s) in RCA: 203] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2009] [Revised: 11/11/2009] [Accepted: 11/16/2009] [Indexed: 10/20/2022]
Abstract
The strategies organisms use to decode synonymous codons in cytosolic protein synthesis are not uniform. The complete isoacceptor tRNA repertoire and the type of modified nucleoside found at the wobble position 34 of their anticodons were analyzed in all kingdoms of life. This led to the identification of four main decoding strategies that are diversely used in Bacteria, Archaea and Eukarya. Many of the modern tRNA modification enzymes acting at position 34 of tRNAs are present only in specific domains and obviously have arisen late during evolution. In an evolutionary fine-tuning process, these enzymes must have played an essential role in the progressive introduction of new amino acids, and in the refinement and standardization of the canonical nuclear genetic code observed in all extant organisms (functional convergent evolutionary hypothesis).
Collapse
Affiliation(s)
- Henri Grosjean
- Université Paris-Sud, CNRS, UMR8621, Institut de Génétique et de Microbiologie, Orsay F-91405, France.
| | | | | |
Collapse
|
49
|
Fu H, Liu LG, Peng JP, Leng WC, Yang J, Jin Q. Transcriptional profile of the Shigella flexneri response to an alkaloid: berberine. FEMS Microbiol Lett 2009; 303:169-75. [PMID: 20030725 DOI: 10.1111/j.1574-6968.2009.01872.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Berberine, a natural isoquinoline alkaloid found in many medicinal herbs, has been shown to be active against a variety of microbial infections. To examine the potential effects of berberine on Shigella flexneri, a whole-genome DNA microarray was constructed and a transcriptome analysis of the cellular responses of S. flexneri when exposed to berberine chloride (BC) was performed. Our data revealed that BC upregulated a group of genes involved in DNA replication, repair and division. Intriguingly, the expression of many genes related to cell envelope biogenesis was increased. In addition, many genes involved in cell secretion, nucleotide metabolism, translation, fatty acid metabolism and the virulence system were also induced by the drug. However, more genes from the functional classes of carbohydrate metabolism, energy production and conversion as well as amino acid metabolism were significantly repressed than were induced. These results provide a comprehensive view of the changes in gene expression when S. flexneri was exposed to BC, and shed light on its complicated effects on this pathogen.
Collapse
Affiliation(s)
- Hua Fu
- State Key Laboratory for Molecular Virology and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy of Medical Sciences, Beijing, China
| | | | | | | | | | | |
Collapse
|
50
|
Urm1 at the crossroad of modifications. 'Protein Modifications: Beyond the Usual Suspects' Review Series. EMBO Rep 2009; 9:1196-202. [PMID: 19047990 DOI: 10.1038/embor.2008.209] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2008] [Accepted: 10/20/2008] [Indexed: 11/08/2022] Open
Abstract
The ubiquitin-like protein Urm1 can be covalently conjugated to other proteins, such as the yeast thioredoxin peroxidase protein Ahp1p, through a mechanism involving the ubiquitin E1-like enzyme Uba4. Recent findings have revealed a second function of Urm1 as a sulphur carrier in the thiolation of eukaryotic cytoplasmic transfer RNAs (tRNAs). Interestingly, this new role of Urm1 is similar to the sulphur-carrier activity of its prokaryotic counterparts, strengthening the hypothesis that Urm1 is a molecular fossil of the ubiquitin-like protein family. Here, we discuss the function of Urm1 in light of its dual role in protein and RNA modification.
Collapse
|