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Toubdji S, Thullier Q, Kilz LM, Marchand V, Yuan Y, Sudol C, Goyenvalle C, Jean-Jean O, Rose S, Douthwaite S, Hardy L, Baharoglu Z, de Crécy-Lagard V, Helm M, Motorin Y, Hamdane D, Brégeon D. Exploring a unique class of flavoenzymes: Identification and biochemical characterization of ribosomal RNA dihydrouridine synthase. Proc Natl Acad Sci U S A 2024; 121:e2401981121. [PMID: 39078675 PMCID: PMC11317573 DOI: 10.1073/pnas.2401981121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 06/20/2024] [Indexed: 07/31/2024] Open
Abstract
Dihydrouridine (D), a prevalent and evolutionarily conserved base in the transcriptome, primarily resides in tRNAs and, to a lesser extent, in mRNAs. Notably, this modification is found at position 2449 in the Escherichia coli 23S rRNA, strategically positioned near the ribosome's peptidyl transferase site. Despite the prior identification, in E. coli genome, of three dihydrouridine synthases (DUS), a set of NADPH and FMN-dependent enzymes known for introducing D in tRNAs and mRNAs, characterization of the enzyme responsible for D2449 deposition has remained elusive. This study introduces a rapid method for detecting D in rRNA, involving reverse transcriptase-blockage at the rhodamine-labeled D2449 site, followed by PCR amplification (RhoRT-PCR). Through analysis of rRNA from diverse E. coli strains, harboring chromosomal or single-gene deletions, we pinpoint the yhiN gene as the ribosomal dihydrouridine synthase, now designated as RdsA. Biochemical characterizations uncovered RdsA as a unique class of flavoenzymes, dependent on FAD and NADH, with a complex structural topology. In vitro assays demonstrated that RdsA dihydrouridylates a short rRNA transcript mimicking the local structure of the peptidyl transferase site. This suggests an early introduction of this modification before ribosome assembly. Phylogenetic studies unveiled the widespread distribution of the yhiN gene in the bacterial kingdom, emphasizing the conservation of rRNA dihydrouridylation. In a broader context, these findings underscore nature's preference for utilizing reduced flavin in the reduction of uridines and their derivatives.
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Affiliation(s)
- Sabrine Toubdji
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Biology of Aging and Adaptation, Institut de Biologie Paris-Seine, F-75252Paris Cedex 05, France
- Collège De France, Sorbonne Université, CNRS, Laboratoire de Chimie des Processus Biologiques, F-75231, Paris Cedex 05, France
| | - Quentin Thullier
- Université de Lorraine, CNRS, Institut National de la Santé et de la Recherche Médicale, Ingénierie-Biologie-Santé en Lorraine, Epitranscriptomique et Séquençage Core Facility, F-54000Nancy, France
- Université de Lorraine, CNRS, Ingénierie Moléculaire, Cellulaire et Physiopathologie, F-54000Nancy, France
| | - Lea-Marie Kilz
- Institut für Pharmazeutische und Biomedizinische Wissenschaften, Johannes Gutenberg-Universität, MainzD-55128, Germany
| | - Virginie Marchand
- Université de Lorraine, CNRS, Institut National de la Santé et de la Recherche Médicale, Ingénierie-Biologie-Santé en Lorraine, Epitranscriptomique et Séquençage Core Facility, F-54000Nancy, France
- Université de Lorraine, CNRS, Ingénierie Moléculaire, Cellulaire et Physiopathologie, F-54000Nancy, France
| | - Yifeng Yuan
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL32611
| | - Claudia Sudol
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Biology of Aging and Adaptation, Institut de Biologie Paris-Seine, F-75252Paris Cedex 05, France
- Collège De France, Sorbonne Université, CNRS, Laboratoire de Chimie des Processus Biologiques, F-75231, Paris Cedex 05, France
| | - Catherine Goyenvalle
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Biology of Aging and Adaptation, Institut de Biologie Paris-Seine, F-75252Paris Cedex 05, France
| | - Olivier Jean-Jean
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Biology of Aging and Adaptation, Institut de Biologie Paris-Seine, F-75252Paris Cedex 05, France
| | - Simon Rose
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230Odense M, Denmark
| | - Stephen Douthwaite
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230Odense M, Denmark
| | - Léo Hardy
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, F-75015 Paris, France
| | - Zeynep Baharoglu
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, F-75015 Paris, France
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL32611
- Genetics Institute, University of Florida, Gainesville, FL32610
| | - Mark Helm
- Institut für Pharmazeutische und Biomedizinische Wissenschaften, Johannes Gutenberg-Universität, MainzD-55128, Germany
| | - Yuri Motorin
- Université de Lorraine, CNRS, Institut National de la Santé et de la Recherche Médicale, Ingénierie-Biologie-Santé en Lorraine, Epitranscriptomique et Séquençage Core Facility, F-54000Nancy, France
- Université de Lorraine, CNRS, Ingénierie Moléculaire, Cellulaire et Physiopathologie, F-54000Nancy, France
| | - Djemel Hamdane
- Collège De France, Sorbonne Université, CNRS, Laboratoire de Chimie des Processus Biologiques, F-75231, Paris Cedex 05, France
| | - Damien Brégeon
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Biology of Aging and Adaptation, Institut de Biologie Paris-Seine, F-75252Paris Cedex 05, France
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2
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Schultz SK, Kothe U. RNA modifying enzymes shape tRNA biogenesis and function. J Biol Chem 2024; 300:107488. [PMID: 38908752 PMCID: PMC11301382 DOI: 10.1016/j.jbc.2024.107488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 06/24/2024] Open
Abstract
Transfer RNAs (tRNAs) are the most highly modified cellular RNAs, both with respect to the proportion of nucleotides that are modified within the tRNA sequence and with respect to the extraordinary diversity in tRNA modification chemistry. However, the functions of many different tRNA modifications are only beginning to emerge. tRNAs have two general clusters of modifications. The first cluster is within the anticodon stem-loop including several modifications essential for protein translation. The second cluster of modifications is within the tRNA elbow, and roles for these modifications are less clear. In general, tRNA elbow modifications are typically not essential for cell growth, but nonetheless several tRNA elbow modifications have been highly conserved throughout all domains of life. In addition to forming modifications, many tRNA modifying enzymes have been demonstrated or hypothesized to also play an important role in folding tRNA acting as tRNA chaperones. In this review, we summarize the known functions of tRNA modifying enzymes throughout the lifecycle of a tRNA molecule, from transcription to degradation. Thereby, we describe how tRNA modification and folding by tRNA modifying enzymes enhance tRNA maturation, tRNA aminoacylation, and tRNA function during protein synthesis, ultimately impacting cellular phenotypes and disease.
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Affiliation(s)
- Sarah K Schultz
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada; Alberta RNA Research and Training Institute (ARRTI), Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada.
| | - Ute Kothe
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada; Alberta RNA Research and Training Institute (ARRTI), Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada.
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3
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Sudol C, Kilz LM, Marchand V, Thullier Q, Guérineau V, Goyenvalle C, Faivre B, Toubdji S, Lombard M, Jean-Jean O, de Crécy-Lagard V, Helm M, Motorin Y, Brégeon D, Hamdane D. Functional redundancy in tRNA dihydrouridylation. Nucleic Acids Res 2024; 52:5880-5894. [PMID: 38682613 PMCID: PMC11162810 DOI: 10.1093/nar/gkae325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 03/26/2024] [Accepted: 04/24/2024] [Indexed: 05/01/2024] Open
Abstract
Dihydrouridine (D) is a common modified base found predominantly in transfer RNA (tRNA). Despite its prevalence, the mechanisms underlying dihydrouridine biosynthesis, particularly in prokaryotes, have remained elusive. Here, we conducted a comprehensive investigation into D biosynthesis in Bacillus subtilis through a combination of genetic, biochemical, and epitranscriptomic approaches. Our findings reveal that B. subtilis relies on two FMN-dependent Dus-like flavoprotein homologs, namely DusB1 and DusB2, to introduce all D residues into its tRNAs. Notably, DusB1 exhibits multisite enzyme activity, enabling D formation at positions 17, 20, 20a and 47, while DusB2 specifically catalyzes D biosynthesis at positions 20 and 20a, showcasing a functional redundancy among modification enzymes. Extensive tRNA-wide D-mapping demonstrates that this functional redundancy impacts the majority of tRNAs, with DusB2 displaying a higher dihydrouridylation efficiency compared to DusB1. Interestingly, we found that BsDusB2 can function like a BsDusB1 when overexpressed in vivo and under increasing enzyme concentration in vitro. Furthermore, we establish the importance of the D modification for B. subtilis growth at suboptimal temperatures. Our study expands the understanding of D modifications in prokaryotes, highlighting the significance of functional redundancy in this process and its impact on bacterial growth and adaptation.
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Affiliation(s)
- Claudia Sudol
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Biology of Aging and Adaptation, Paris 75252, France
- Collège De France, Sorbonne Université, CNRS, Laboratoire de Chimie des Processus Biologiques, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Lea-Marie Kilz
- Institut für pharmazeutische und biomedizinische Wissenschaften (IPBW), Johannes Gutenberg-Universität, Mainz 55128, Germany
| | - Virginie Marchand
- Université de Lorraine, CNRS, INSERM, UMS2008/US40 IBSLor, EpiRNA-Seq Core Facility, Nancy F-54000, France
- Université de Lorraine, CNRS, UMR7365 IMoPA, Nancy F-54000, France
| | - Quentin Thullier
- Université de Lorraine, CNRS, INSERM, UMS2008/US40 IBSLor, EpiRNA-Seq Core Facility, Nancy F-54000, France
- Université de Lorraine, CNRS, UMR7365 IMoPA, Nancy F-54000, France
| | - Vincent Guérineau
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198, Gif-sur-Yvette, France
| | - Catherine Goyenvalle
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Biology of Aging and Adaptation, Paris 75252, France
| | - Bruno Faivre
- Collège De France, Sorbonne Université, CNRS, Laboratoire de Chimie des Processus Biologiques, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Sabrine Toubdji
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Biology of Aging and Adaptation, Paris 75252, France
- Collège De France, Sorbonne Université, CNRS, Laboratoire de Chimie des Processus Biologiques, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Murielle Lombard
- Collège De France, Sorbonne Université, CNRS, Laboratoire de Chimie des Processus Biologiques, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Olivier Jean-Jean
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Biology of Aging and Adaptation, Paris 75252, France
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
- University of Florida, Genetics Institute, Gainesville, FL 32610, USA
| | - Mark Helm
- Institut für pharmazeutische und biomedizinische Wissenschaften (IPBW), Johannes Gutenberg-Universität, Mainz 55128, Germany
| | - Yuri Motorin
- Université de Lorraine, CNRS, INSERM, UMS2008/US40 IBSLor, EpiRNA-Seq Core Facility, Nancy F-54000, France
- Université de Lorraine, CNRS, UMR7365 IMoPA, Nancy F-54000, France
| | - Damien Brégeon
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Biology of Aging and Adaptation, Paris 75252, France
| | - Djemel Hamdane
- Collège De France, Sorbonne Université, CNRS, Laboratoire de Chimie des Processus Biologiques, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
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4
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Ji J, Yu NJ, Kleiner RE. Sequence- and Structure-Specific tRNA Dihydrouridylation by hDUS2. ACS CENTRAL SCIENCE 2024; 10:803-812. [PMID: 38680565 PMCID: PMC11046453 DOI: 10.1021/acscentsci.3c01382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 05/01/2024]
Abstract
The post-transcriptional reduction of uridine to dihydrouridine (D) by dihydrouridine synthase (DUS) enzymes is among the most ubiquitous transformations in RNA biology. D is found at multiple sites in tRNAs, and studies in yeast have proposed that each of the four eukaryotic DUS enzymes modifies a different site; however, the molecular basis for this exquisite selectivity is unknown, and human DUS enzymes have remained largely uncharacterized. Here we investigate the substrate specificity of human dihydrouridine synthase 2 (hDUS2) using mechanism-based cross-linking with 5-bromouridine (5-BrUrd)-modified oligonucleotide probes and in vitro dihydrouridylation assays. We find that hDUS2 exclusively modifies U20 across diverse tRNA substrates and identify a minimal GU sequence within the tRNA D loop that underlies selective substrate modification. Further, we use our mechanism-based platform to screen small molecule inhibitors of hDUS2, a potential anticancer target. Our work elucidates the principles of substrate modification by a conserved DUS and provides a general platform for studying RNA modifying enzymes with sequence-defined activity-based probes.
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Affiliation(s)
- Jingwei Ji
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Nathan J. Yu
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Ralph E. Kleiner
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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5
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Harun-Or-Roshid M, Maeda K, Phan LT, Manavalan B, Kurata H. Stack-DHUpred: Advancing the accuracy of dihydrouridine modification sites detection via stacking approach. Comput Biol Med 2024; 169:107848. [PMID: 38145601 DOI: 10.1016/j.compbiomed.2023.107848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 11/14/2023] [Accepted: 12/11/2023] [Indexed: 12/27/2023]
Abstract
Dihydrouridine (DHU, D) is one of the most abundant post-transcriptional uridine modifications found in tRNA, mRNA, and snoRNA, closely associated with disease pathogenesis and various biological processes in eukaryotes. Identifying D sites is important for understanding the modification mechanisms and/or epigenetic regulation. However, biological experiments for detecting D sites are time-consuming and expensive. Given these challenges, computational methods have been developed for accurately identifying the D sites in genome-wide datasets. However, existing methods have some limitations, and their prediction performance needs to be improved. In this work, we have developed a new computational predictor for accurately identifying D sites called Stack-DHUpred. Briefly, we trained 66 baseline models or single-feature models by connecting six machine learning classifiers with eleven different feature encoding methods and stacked different baseline models to build stacked ensemble learning models. Subsequently, the optimal combination of the baseline models was identified for the construction of the final stacked model. Remarkably, the Stack-DHUpred outperformed the existing predictors on our new independent dataset, indicating that the stacking approach significantly improved the prediction performance. We have made Stack-DHUpred available to the public through a web server (http://kurata35.bio.kyutech.ac.jp/Stack-DHUpred) and a standalone program (https://github.com/kuratahiroyuki/Stack-DHUpred). We believe that Stack-DHUpred will be a valuable tool for accelerating the discovery of D modifications and understanding their role in post-transcriptional regulation.
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Affiliation(s)
- Md Harun-Or-Roshid
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan
| | - Kazuhiro Maeda
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan
| | - Le Thi Phan
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Balachandran Manavalan
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
| | - Hiroyuki Kurata
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan.
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6
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Yu NJ, Dai W, Li A, He M, Kleiner RE. Cell type-specific translational regulation by human DUS enzymes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.03.565399. [PMID: 37965204 PMCID: PMC10635104 DOI: 10.1101/2023.11.03.565399] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Dihydrouridine is an abundant and conserved modified nucleoside present on tRNA, but characterization and functional studies of modification sites and associated DUS writer enzymes in mammals is lacking. Here we use a chemical probing strategy, RNABPP-PS, to identify 5-chlorouridine as an activity-based probe for human DUS enzymes. We map D modifications using RNA-protein crosslinking and chemical transformation and mutational profiling to reveal D modification sites on human tRNAs. Further, we knock out individual DUS genes in two human cell lines to investigate regulation of tRNA expression levels and codon-specific translation. We show that whereas D modifications are present across most tRNA species, loss of D only perturbs the translational function of a subset of tRNAs in a cell type-specific manner. Our work provides powerful chemical strategies for investigating D and DUS enzymes in diverse biological systems and provides insight into the role of a ubiquitous tRNA modification in translational regulation.
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7
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Ji J, Yu NJ, Kleiner RE. A minimal sequence motif drives selective tRNA dihydrouridylation by hDUS2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.04.565616. [PMID: 37961591 PMCID: PMC10635142 DOI: 10.1101/2023.11.04.565616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The post-transcriptional reduction of uridine to dihydrouridine (D) by dihydrouridine synthase (DUS) enzymes is among the most ubiquitous transformations in RNA biology. D is found at multiple sites in tRNAs and studies in yeast have proposed that each of the four eukaryotic DUS enzymes modifies a different site, however the molecular basis for this exquisite selectivity is unknown and human DUS enzymes have remained largely uncharacterized. Here we investigate the substrate specificity of human dihydrouridine synthase 2 (hDUS2) using mechanism-based crosslinking with 5-bromouridine (5-BrUrd)-modified oligonucleotide probes and in vitro dihydrouridylation assays. We find that hDUS2 modifies U20 in the D loop of diverse tRNA substrates and identify a minimal GU motif within the tRNA tertiary fold required for directing its activity. Further, we use our mechanism-based platform to screen small molecule inhibitors of hDUS2, a potential anti-cancer target. Our work elucidates the principles of substrate modification by a conserved DUS and provides a general platform to studying RNA modifying enzymes with sequence-defined activity-based probes.
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8
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Dai W, Yu NJ, Kleiner RE. Chemoproteomic Approaches to Studying RNA Modification-Associated Proteins. Acc Chem Res 2023; 56:2726-2739. [PMID: 37733063 PMCID: PMC11025531 DOI: 10.1021/acs.accounts.3c00450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
The function of cellular RNA is modulated by a host of post-transcriptional chemical modifications installed by dedicated RNA-modifying enzymes. RNA modifications are widespread in biology, occurring in all kingdoms of life and in all classes of RNA molecules. They regulate RNA structure, folding, and protein-RNA interactions, and have important roles in fundamental gene expression processes involving mRNA, tRNA, rRNA, and other types of RNA species. Our understanding of RNA modifications has advanced considerably; however, there are still many outstanding questions regarding the distribution of modifications across all RNA transcripts and their biological function. One of the major challenges in the study of RNA modifications is the lack of sequencing methods for the transcriptome-wide mapping of different RNA-modification structures. Furthermore, we lack general strategies to characterize RNA-modifying enzymes and RNA-modification reader proteins. Therefore, there is a need for new approaches to enable integrated studies of RNA-modification chemistry and biology.In this Account, we describe our development and application of chemoproteomic strategies for the study of RNA-modification-associated proteins. We present two orthogonal methods based on nucleoside and oligonucleotide chemical probes: 1) RNA-mediated activity-based protein profiling (RNABPP), a metabolic labeling strategy based on reactive modified nucleoside probes to profile RNA-modifying enzymes in cells and 2) photo-cross-linkable diazirine-containing synthetic oligonucleotide probes for identifying RNA-modification reader proteins.We use RNABPP with C5-modified cytidine and uridine nucleosides to capture diverse RNA-pyrimidine-modifying enzymes including methyltransferases, dihydrouridine synthases, and RNA dioxygenase enzymes. Metabolic labeling facilitates the mechanism-based cross-linking of RNA-modifying enzymes with their native RNA substrates in cells. Covalent RNA-protein complexes are then isolated by denaturing oligo(dT) pulldown, and cross-linked proteins are identified by quantitative proteomics. Once suitable modified nucleosides have been identified as mechanism-based proteomic probes, they can be further deployed in transcriptome-wide sequencing experiments to profile the substrates of RNA-modifying enzymes at nucleotide resolution. Using 5-fluorouridine-mediated RNA-protein cross-linking and sequencing, we analyzed the substrates of human dihydrouridine synthase DUS3L. 5-Ethynylcytidine-mediated cross-linking enabled the investigation of ALKBH1 substrates. We also characterized the functions of these RNA-modifying enzymes in human cells by using genetic knockouts and protein translation reporters.We profiled RNA readers for N6-methyladenosine (m6A) and N1-methyladenosine (m1A) using a comparative proteomic workflow based on diazirine-containing modified oligonucleotide probes. Our approach enables quantitative proteome-wide analysis of the preference of RNA-binding proteins for modified nucleotides across a range of affinities. Interestingly, we found that YTH-domain proteins YTHDF1/2 can bind to both m6A and m1A to mediate transcript destabilization. Furthermore, m6A also inhibits stress granule proteins from binding to RNA.Taken together, we demonstrate the application of chemical probing strategies, together with proteomic and transcriptomic workflows, to reveal new insights into the biological roles of RNA modifications and their associated proteins.
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Affiliation(s)
| | | | - Ralph E. Kleiner
- Department of Chemistry, Princeton University, Princeton, NJ, USA 08544
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9
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Patrasso EA, Raikundalia S, Arango D. Regulation of the epigenome through RNA modifications. Chromosoma 2023; 132:231-246. [PMID: 37138119 PMCID: PMC10524150 DOI: 10.1007/s00412-023-00794-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/10/2023] [Accepted: 04/12/2023] [Indexed: 05/05/2023]
Abstract
Chemical modifications of nucleotides expand the complexity and functional properties of genomes and transcriptomes. A handful of modifications in DNA bases are part of the epigenome, wherein DNA methylation regulates chromatin structure, transcription, and co-transcriptional RNA processing. In contrast, more than 150 chemical modifications of RNA constitute the epitranscriptome. Ribonucleoside modifications comprise a diverse repertoire of chemical groups, including methylation, acetylation, deamination, isomerization, and oxidation. Such RNA modifications regulate all steps of RNA metabolism, including folding, processing, stability, transport, translation, and RNA's intermolecular interactions. Initially thought to influence all aspects of the post-transcriptional regulation of gene expression exclusively, recent findings uncovered a crosstalk between the epitranscriptome and the epigenome. In other words, RNA modifications feedback to the epigenome to transcriptionally regulate gene expression. The epitranscriptome achieves this feat by directly or indirectly affecting chromatin structure and nuclear organization. This review highlights how chemical modifications in chromatin-associated RNAs (caRNAs) and messenger RNAs (mRNAs) encoding factors involved in transcription, chromatin structure, histone modifications, and nuclear organization affect gene expression transcriptionally.
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Affiliation(s)
- Emmely A Patrasso
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Medical and Pharmaceutical Biotechnology Program, IMC University of Applied Sciences, Krems, Austria
| | - Sweta Raikundalia
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Daniel Arango
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA.
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10
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Biela A, Hammermeister A, Kaczmarczyk I, Walczak M, Koziej L, Lin TY, Glatt S. The diverse structural modes of tRNA binding and recognition. J Biol Chem 2023; 299:104966. [PMID: 37380076 PMCID: PMC10424219 DOI: 10.1016/j.jbc.2023.104966] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 06/20/2023] [Accepted: 06/22/2023] [Indexed: 06/30/2023] Open
Abstract
tRNAs are short noncoding RNAs responsible for decoding mRNA codon triplets, delivering correct amino acids to the ribosome, and mediating polypeptide chain formation. Due to their key roles during translation, tRNAs have a highly conserved shape and large sets of tRNAs are present in all living organisms. Regardless of sequence variability, all tRNAs fold into a relatively rigid three-dimensional L-shaped structure. The conserved tertiary organization of canonical tRNA arises through the formation of two orthogonal helices, consisting of the acceptor and anticodon domains. Both elements fold independently to stabilize the overall structure of tRNAs through intramolecular interactions between the D- and T-arm. During tRNA maturation, different modifying enzymes posttranscriptionally attach chemical groups to specific nucleotides, which not only affect translation elongation rates but also restrict local folding processes and confer local flexibility when required. The characteristic structural features of tRNAs are also employed by various maturation factors and modification enzymes to assure the selection, recognition, and positioning of specific sites within the substrate tRNAs. The cellular functional repertoire of tRNAs continues to extend well beyond their role in translation, partly, due to the expanding pool of tRNA-derived fragments. Here, we aim to summarize the most recent developments in the field to understand how three-dimensional structure affects the canonical and noncanonical functions of tRNA.
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Affiliation(s)
- Anna Biela
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Igor Kaczmarczyk
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland; Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - Marta Walczak
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland; Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - Lukasz Koziej
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Ting-Yu Lin
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
| | - Sebastian Glatt
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
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11
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Leiva LE, Zegarra V, Bange G, Ibba M. At the Crossroad of Nucleotide Dynamics and Protein Synthesis in Bacteria. Microbiol Mol Biol Rev 2023; 87:e0004422. [PMID: 36853029 PMCID: PMC10029340 DOI: 10.1128/mmbr.00044-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
Nucleotides are at the heart of the most essential biological processes in the cell, be it as key protagonists in the dogma of molecular biology or by regulating multiple metabolic pathways. The dynamic nature of nucleotides, the cross talk between them, and their constant feedback to and from the cell's metabolic state position them as a hallmark of adaption toward environmental and growth challenges. It has become increasingly clear how the activity of RNA polymerase, the synthesis and maintenance of tRNAs, mRNA translation at all stages, and the biogenesis and assembly of ribosomes are fine-tuned by the pools of intracellular nucleotides. With all aspects composing protein synthesis involved, the ribosome emerges as the molecular hub in which many of these nucleotides encounter each other and regulate the state of the cell. In this review, we aim to highlight intracellular nucleotides in bacteria as dynamic characters permanently cross talking with each other and ultimately regulating protein synthesis at various stages in which the ribosome is mainly the principal character.
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Affiliation(s)
- Lorenzo Eugenio Leiva
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Victor Zegarra
- Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Gert Bange
- Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Michael Ibba
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
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12
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Wang Y, Wang X, Cui X, Meng J, Rong R. Self-attention enabled deep learning of dihydrouridine (D) modification on mRNAs unveiled a distinct sequence signature from tRNAs. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 31:411-420. [PMID: 36845339 PMCID: PMC9945750 DOI: 10.1016/j.omtn.2023.01.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 01/23/2023] [Indexed: 01/28/2023]
Abstract
Dihydrouridine (D) is a modified pyrimidine nucleotide universally found in viral, prokaryotic, and eukaryotic species. It serves as a metabolic modulator for various pathological conditions, and its elevated levels in tumors are associated with a series of cancers. Precise identification of D sites on RNA is vital for understanding its biological function. A number of computational approaches have been developed for predicting D sites on tRNAs; however, none have considered mRNAs. We present here DPred, the first computational tool for predicting D on mRNAs in yeast from the primary RNA sequences. Built on a local self-attention layer and a convolutional neural network (CNN) layer, the proposed deep learning model outperformed classic machine learning approaches (random forest, support vector machines, etc.) and achieved reasonable accuracy and reliability with areas under the curve of 0.9166 and 0.9027 in jackknife cross-validation and on an independent testing dataset, respectively. Importantly, we showed that distinct sequence signatures are associated with the D sites on mRNAs and tRNAs, implying potentially different formation mechanisms and putative divergent functionality of this modification on the two types of RNA. DPred is available as a user-friendly Web server.
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Affiliation(s)
- Yue Wang
- Department of Mathematical Sciences, Xi’an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China,Department of Computer Science, University of Liverpool, L69 7ZB Liverpool, UK
| | - Xuan Wang
- Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
| | - Xiaodong Cui
- School of Marine Science and Technology, Northwestern Polytechnical University, Xi’an, Shaanxi 710072, China
| | - Jia Meng
- Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China,AI University Research Centre, Xi’an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China,Institute of Systems, Molecular and Integrative Biology, University of Liverpool, L69 7ZB Liverpool, UK
| | - Rong Rong
- Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China,Corresponding author: Rong Rong, Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China.
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13
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Lombard M, Reed CJ, Pecqueur L, Faivre B, Toubdji S, Sudol C, Brégeon D, de Crécy-Lagard V, Hamdane D. Evolutionary Diversity of Dus2 Enzymes Reveals Novel Structural and Functional Features among Members of the RNA Dihydrouridine Synthases Family. Biomolecules 2022; 12:1760. [PMID: 36551188 PMCID: PMC9775027 DOI: 10.3390/biom12121760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
Dihydrouridine (D) is an abundant modified base found in the tRNAs of most living organisms and was recently detected in eukaryotic mRNAs. This base confers significant conformational plasticity to RNA molecules. The dihydrouridine biosynthetic reaction is catalyzed by a large family of flavoenzymes, the dihydrouridine synthases (Dus). So far, only bacterial Dus enzymes and their complexes with tRNAs have been structurally characterized. Understanding the structure-function relationships of eukaryotic Dus proteins has been hampered by the paucity of structural data. Here, we combined extensive phylogenetic analysis with high-precision 3D molecular modeling of more than 30 Dus2 enzymes selected along the tree of life to determine the evolutionary molecular basis of D biosynthesis by these enzymes. Dus2 is the eukaryotic enzyme responsible for the synthesis of D20 in tRNAs and is involved in some human cancers and in the detoxification of β-amyloid peptides in Alzheimer's disease. In addition to the domains forming the canonical structure of all Dus, i.e., the catalytic TIM-barrel domain and the helical domain, both participating in RNA recognition in the bacterial Dus, a majority of Dus2 proteins harbor extensions at both ends. While these are mainly unstructured extensions on the N-terminal side, the C-terminal side extensions can adopt well-defined structures such as helices and beta-sheets or even form additional domains such as zinc finger domains. 3D models of Dus2/tRNA complexes were also generated. This study suggests that eukaryotic Dus2 proteins may have an advantage in tRNA recognition over their bacterial counterparts due to their modularity.
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Affiliation(s)
- Murielle Lombard
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège de France, Université Pierre et Marie Curie, 11 Place Marcelin Berthelot, CEDEX 05, 75231 Paris, France
| | - Colbie J. Reed
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Ludovic Pecqueur
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège de France, Université Pierre et Marie Curie, 11 Place Marcelin Berthelot, CEDEX 05, 75231 Paris, France
| | - Bruno Faivre
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège de France, Université Pierre et Marie Curie, 11 Place Marcelin Berthelot, CEDEX 05, 75231 Paris, France
| | - Sabrine Toubdji
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège de France, Université Pierre et Marie Curie, 11 Place Marcelin Berthelot, CEDEX 05, 75231 Paris, France
- IBPS, Biology of Aging and Adaptation, Sorbonne Université 7 quai Saint Bernard, CEDEX 05, 75252 Paris, France
| | - Claudia Sudol
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège de France, Université Pierre et Marie Curie, 11 Place Marcelin Berthelot, CEDEX 05, 75231 Paris, France
- IBPS, Biology of Aging and Adaptation, Sorbonne Université 7 quai Saint Bernard, CEDEX 05, 75252 Paris, France
| | - Damien Brégeon
- IBPS, Biology of Aging and Adaptation, Sorbonne Université 7 quai Saint Bernard, CEDEX 05, 75252 Paris, France
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Djemel Hamdane
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège de France, Université Pierre et Marie Curie, 11 Place Marcelin Berthelot, CEDEX 05, 75231 Paris, France
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14
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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.
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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.)
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15
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Brégeon D, Pecqueur L, Toubdji S, Sudol C, Lombard M, Fontecave M, de Crécy-Lagard V, Motorin Y, Helm M, Hamdane D. Dihydrouridine in the Transcriptome: New Life for This Ancient RNA Chemical Modification. ACS Chem Biol 2022; 17:1638-1657. [PMID: 35737906 DOI: 10.1021/acschembio.2c00307] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Until recently, post-transcriptional modifications of RNA were largely restricted to noncoding RNA species. However, this belief seems to have quickly dissipated with the growing number of new modifications found in mRNA that were originally thought to be primarily tRNA-specific, such as dihydrouridine. Recently, transcriptomic profiling, metabolic labeling, and proteomics have identified unexpected dihydrouridylation of mRNAs, greatly expanding the catalog of novel mRNA modifications. These data also implicated dihydrouridylation in meiotic chromosome segregation, protein translation rates, and cell proliferation. Dihydrouridylation of tRNAs and mRNAs are introduced by flavin-dependent dihydrouridine synthases. In this review, we will briefly outline the current knowledge on the distribution of dihydrouridines in the transcriptome, their chemical labeling, and highlight structural and mechanistic aspects regarding the dihydrouridine synthases enzyme family. A special emphasis on important research directions to be addressed will also be discussed. This new entry of dihydrouridine into mRNA modifications has definitely added a new layer of information that controls protein synthesis.
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Affiliation(s)
- Damien Brégeon
- IBPS, Biology of Aging and Adaptation, Sorbonne Université, Paris 75252, France
| | - Ludovic Pecqueur
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et Marie Curie, 11 place Marcelin Berthelot, 75231 Paris, Cedex 05, France
| | - Sabrine Toubdji
- IBPS, Biology of Aging and Adaptation, Sorbonne Université, Paris 75252, France
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et Marie Curie, 11 place Marcelin Berthelot, 75231 Paris, Cedex 05, France
| | - Claudia Sudol
- IBPS, Biology of Aging and Adaptation, Sorbonne Université, Paris 75252, France
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et Marie Curie, 11 place Marcelin Berthelot, 75231 Paris, Cedex 05, France
| | - Murielle Lombard
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et Marie Curie, 11 place Marcelin Berthelot, 75231 Paris, Cedex 05, France
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et Marie Curie, 11 place Marcelin Berthelot, 75231 Paris, Cedex 05, France
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611, United States
- Genetics Institute, University of Florida, Gainesville, Florida 32610, United States
| | - Yuri Motorin
- Université de Lorraine, CNRS, INSERM, UMS2008/US40 IBSLor, EpiRNA-Seq Core Facility, Nancy F-54000, France
- Université de Lorraine, CNRS, UMR7365 IMoPA, Nancy F-54000, France
| | - Mark Helm
- Institut für pharmazeutische und biomedizinische Wissenschaften (IPBW), Johannes Gutenberg-Universität, Mainz 55128, Germany
| | - Djemel Hamdane
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et Marie Curie, 11 place Marcelin Berthelot, 75231 Paris, Cedex 05, France
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16
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Finet O, Yague-Sanz C, Marchand F, Hermand D. The Dihydrouridine landscape from tRNA to mRNA: a perspective on synthesis, structural impact and function. RNA Biol 2022; 19:735-750. [PMID: 35638108 PMCID: PMC9176250 DOI: 10.1080/15476286.2022.2078094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The universal dihydrouridine (D) epitranscriptomic mark results from a reduction of uridine by the Dus family of NADPH-dependent reductases and is typically found within the eponym D-loop of tRNAs. Despite its apparent simplicity, D is structurally unique, with the potential to deeply affect the RNA backbone and many, if not all, RNA-connected processes. The first landscape of its occupancy within the tRNAome was reported 20 years ago. Its potential biological significance was highlighted by observations ranging from a strong bias in its ecological distribution to the predictive nature of Dus enzymes overexpression for worse cancer patient outcomes. The exquisite specificity of the Dus enzymes revealed by a structure-function analyses and accumulating clues that the D distribution may expand beyond tRNAs recently led to the development of new high-resolution mapping methods, including Rho-seq that established the presence of D within mRNAs and led to the demonstration of its critical physiological relevance.
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Affiliation(s)
- Olivier Finet
- URPHYM-GEMO, The University of Namur, Namur, Belgium
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17
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Kelley M, Uhran M, Herbert C, Yoshida G, Watts ER, Limbach PA, Benoit JB. Abundances of transfer RNA modifications and transcriptional levels of tRNA-modifying enzymes are sex-associated in mosquitoes. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2022; 143:103741. [PMID: 35181477 PMCID: PMC9034435 DOI: 10.1016/j.ibmb.2022.103741] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 02/12/2022] [Accepted: 02/13/2022] [Indexed: 06/03/2023]
Abstract
As carriers of multiple human diseases, understanding the mechanisms behind mosquito reproduction may have implications for remediation strategies. Transfer RNA (tRNA) acts as the adapter molecule of amino acids and are key components in protein synthesis. A critical factor in the function of tRNAs is chemical modifications which contribute to codon-anticodon interactions. Here, we provide an assessment of tRNA modifications between sexes for three mosquito species and examine the correlation of transcript levels underlying key proteins involved in tRNA modification. Thirty-three tRNA modifications were detected among mosquito species and most of these modifications are higher in females compared to males for three mosquito species. Analysis of previous male and female RNA-seq datasets indicated a similar increase in transcript levels of tRNA-modifying enzymes in females among six mosquito species, supporting our observed female enrichment of tRNA modifications. Tissues-specific expressional studies revealed higher transcript levels for tRNA-modifying enzymes in the ovaries for Aedes aegypti, but not male reproductive tissues. These studies suggest that tRNA modifications may be critical to reproduction in mosquitoes, representing a potential novel target for control through suppression of fecundity.
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Affiliation(s)
- Melissa Kelley
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45211, USA.
| | - Melissa Uhran
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45211, USA
| | - Cassandra Herbert
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, 45211, USA
| | - George Yoshida
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, 45211, USA
| | - Emmarie R Watts
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45211, USA
| | - Patrick A Limbach
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, 45211, USA
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45211, USA.
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18
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Identification of D Modification Sites Using a Random Forest Model Based on Nucleotide Chemical Properties. Int J Mol Sci 2022; 23:ijms23063044. [PMID: 35328461 PMCID: PMC8950657 DOI: 10.3390/ijms23063044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 02/25/2022] [Accepted: 03/09/2022] [Indexed: 12/03/2022] Open
Abstract
Dihydrouridine (D) is an abundant post-transcriptional modification present in transfer RNA from eukaryotes, bacteria, and archaea. D has contributed to treatments for cancerous diseases. Therefore, the precise detection of D modification sites can enable further understanding of its functional roles. Traditional experimental techniques to identify D are laborious and time-consuming. In addition, there are few computational tools for such analysis. In this study, we utilized eleven sequence-derived feature extraction methods and implemented five popular machine algorithms to identify an optimal model. During data preprocessing, data were partitioned for training and testing. Oversampling was also adopted to reduce the effect of the imbalance between positive and negative samples. The best-performing model was obtained through a combination of random forest and nucleotide chemical property modeling. The optimized model presented high sensitivity and specificity values of 0.9688 and 0.9706 in independent tests, respectively. Our proposed model surpassed published tools in independent tests. Furthermore, a series of validations across several aspects was conducted in order to demonstrate the robustness and reliability of our model.
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19
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Dou L, Zhou W, Zhang L, Xu L, Han K. Accurate identification of RNA D modification using multiple features. RNA Biol 2021; 18:2236-2246. [PMID: 33729104 PMCID: PMC8632091 DOI: 10.1080/15476286.2021.1898160] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 02/13/2021] [Accepted: 02/23/2021] [Indexed: 10/21/2022] Open
Abstract
As one of the common post-transcriptional modifications in tRNAs, dihydrouridine (D) has prominent effects on regulating the flexibility of tRNA as well as cancerous diseases. Facing with the expensive and time-consuming sequencing techniques to detect D modification, precise computational tools can largely promote the progress of molecular mechanisms and medical developments. We proposed a novel predictor, called iRNAD_XGBoost, to identify potential D sites using multiple RNA sequence representations. In this method, by considering the imbalance problem using hybrid sampling method SMOTEEEN, the XGBoost-selected top 30 features are applied to construct model. The optimized model showed high Sn and Sp values of 97.13% and 97.38% over jackknife test, respectively. For the independent experiment, these two metrics separately achieved 91.67% and 94.74%. Compared with iRNAD method, this model illustrated high generalizability and consistent prediction efficiencies for positive and negative samples, which yielded satisfactory MCC scores of 0.94 and 0.86, respectively. It is inferred that the chemical property and nucleotide density features (CPND), electron-ion interaction pseudopotential (EIIP and PseEIIP) as well as dinucleotide composition (DNC) are crucial to the recognition of D modification. The proposed predictor is a promising tool to help experimental biologists investigate molecular functions.
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Affiliation(s)
- Lijun Dou
- School of Automotive and Transportation Engineering, Shenzhen Polytechnic, Shenzhen, GuangdongChina
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, SichuanChina
| | - Wenyang Zhou
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, HeilongjiangChina
| | - Lichao Zhang
- School of Intelligent Manufacturing and Equipment, Shenzhen Institute of Information Technology, Shenzhen, Guangdong, China
| | - Lei Xu
- School of Electronic and Communication Engineering, Shenzhen Polytechnic, Shenzhen, GuangdongChina
| | - Ke Han
- School of Computer and Information Engineering, Harbin University of Commerce, Harbin, HeilongjiangChina
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20
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Wang DO. Epitranscriptomic regulation of cognitive development and decline. Semin Cell Dev Biol 2021; 129:3-13. [PMID: 34857470 DOI: 10.1016/j.semcdb.2021.11.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 11/16/2021] [Accepted: 11/19/2021] [Indexed: 11/24/2022]
Abstract
Functional genomics and systems biology have opened new doors to previously inaccessible genomic information and holistic approaches to study complex networks of genes and proteins in the central nervous system. The advances are revolutionizing our understanding of the genetic underpinning of cognitive development and decline by facilitating identifications of novel molecular regulators and physiological pathways underlying brain function, and by associating polymorphism and mutations to cognitive dysfunction and neurological diseases. However, our current understanding of these complex gene regulatory mechanisms has yet lacked sufficient mechanistic resolution for further translational breakthroughs. Here we review recent findings from the burgeoning field of epitranscriptomics in association of cognitive functions with a special focus on the epitranscritomic regulation in subcellular locations such as chromosome, synapse, and mitochondria. Although there are important gaps in knowledge, current evidence is suggesting that this layer of RNA regulation may be of particular interest for the spatiotemporally coordinated regulation of gene networks in developing and maintaining brain function that underlie cognitive changes.
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Affiliation(s)
- Dan Ohtan Wang
- Center for Biosystems Dynamics Research, RIKEN, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Graduate School of Biostudies, Kyoto University, Yoshida Hon-machi, Kyoto 606-8501, Japan.
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21
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Dai W, Li A, Yu NJ, Nguyen T, Leach RW, Wühr M, Kleiner RE. Activity-based RNA-modifying enzyme probing reveals DUS3L-mediated dihydrouridylation. Nat Chem Biol 2021; 17:1178-1187. [PMID: 34556860 PMCID: PMC8551019 DOI: 10.1038/s41589-021-00874-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 08/02/2021] [Indexed: 11/09/2022]
Abstract
Epitranscriptomic RNA modifications can regulate RNA activity; however, there remains a major gap in our understanding of the RNA chemistry present in biological systems. Here we develop RNA-mediated activity-based protein profiling (RNABPP), a chemoproteomic strategy that relies on metabolic RNA labeling, mRNA interactome capture and quantitative proteomics, to investigate RNA-modifying enzymes in human cells. RNABPP with 5-fluoropyrimidines allowed us to profile 5-methylcytidine (m5C) and 5-methyluridine (m5U) methyltransferases. Further, we uncover a new mechanism-based crosslink between 5-fluorouridine (5-FUrd)-modified RNA and the dihydrouridine synthase (DUS) homolog DUS3L. We investigate the mechanism of crosslinking and use quantitative nucleoside liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis and 5-FUrd-based crosslinking and immunoprecipitation (CLIP) sequencing to map DUS3L-dependent dihydrouridine (DHU) modifications across the transcriptome. Finally, we show that DUS3L-knockout (KO) cells have compromised protein translation rates and impaired cellular proliferation. Taken together, our work provides a general approach for profiling RNA-modifying enzyme activity in living cells and reveals new pathways for epitranscriptomic RNA regulation.
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Affiliation(s)
- Wei Dai
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA,These authors contributed equally
| | - Ang Li
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA,These authors contributed equally
| | - Nathan J. Yu
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Thao Nguyen
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA,Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Robert W. Leach
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Martin Wühr
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Ralph E. Kleiner
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA,
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22
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Guimarães BG, Golinelli-Pimpaneau B. De novo crystal structure determination of double stranded RNA binding domain using only the sulfur anomalous diffraction in SAD phasing. Curr Res Struct Biol 2021; 3:112-120. [PMID: 34235491 PMCID: PMC8244422 DOI: 10.1016/j.crstbi.2021.05.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/07/2021] [Accepted: 05/31/2021] [Indexed: 10/25/2022] Open
Abstract
Single-wavelength anomalous dispersion (SAD)-phasing using sulfur as the unique anomalous scatterer is a powerful method to solve the phase problem in protein crystallography. However, it is not yet widely used by non-expert crystallographers. We report here the structure determination of the double stranded RNA binding domain of human dihydrouridine synthase using the sulfur-SAD method and highly redundant data collected at 1.8 Å ("off-edge"), at which the estimated overall anomalous signal was 1.08%. High multiplicity data were collected on a single crystal rotated along the ϕ or ω axis at different κ angles, with the primary beam intensity being attenuated from 50% to 95%, compared to data collection at 0.98 Å, to reduce radiation damage. SHELXD succeeded to locate 14 out 15 sulfur sites only using the data sets recorded with highest beam attenuation, which provided phases sufficient for structure solving. In an attempt to stimulate the use of sulfur-SAD phasing by a broader community of crystallographers, we describe our experimental strategy together with a compilation of previous successful cases, suggesting that sulfur-SAD phasing should be attempted for determining the de novo structure of any protein with average sulfur content diffracting better than 3 Å resolution.
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Affiliation(s)
| | - Béatrice Golinelli-Pimpaneau
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Sorbonne Université, 11 Place Marcelin Berthelot, 75005 Paris, France
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23
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Faivre B, Lombard M, Fakroun S, Vo CDT, Goyenvalle C, Guérineau V, Pecqueur L, Fontecave M, De Crécy-Lagard V, Brégeon D, Hamdane D. Dihydrouridine synthesis in tRNAs is under reductive evolution in Mollicutes. RNA Biol 2021; 18:2278-2289. [PMID: 33685366 DOI: 10.1080/15476286.2021.1899653] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Dihydrouridine (D) is a tRNA-modified base conserved throughout all kingdoms of life and assuming an important structural role. The conserved dihydrouridine synthases (Dus) carries out D-synthesis. DusA, DusB and DusC are bacterial members, and their substrate specificity has been determined in Escherichia coli. DusA synthesizes D20/D20a while DusB and DusC are responsible for the synthesis of D17 and D16, respectively. Here, we characterize the function of the unique dus gene encoding a DusB detected in Mollicutes, which are bacteria that evolved from a common Firmicute ancestor via massive genome reduction. Using in vitro activity tests as well as in vivo E. coli complementation assays with the enzyme from Mycoplasma capricolum (DusBMCap), a model organism for the study of these parasitic bacteria, we show that, as expected for a DusB homolog, DusBMCap modifies U17 to D17 but also synthetizes D20/D20a combining therefore both E. coli DusA and DusB activities. Hence, this is the first case of a Dus enzyme able to modify up to three different sites as well as the first example of a tRNA-modifying enzyme that can modify bases present on the two opposite sides of an RNA-loop structure. Comparative analysis of the distribution of DusB homologs in Firmicutes revealed the existence of three DusB subgroups namely DusB1, DusB2 and DusB3. The first two subgroups were likely present in the Firmicute ancestor, and Mollicutes have retained DusB1 and lost DusB2. Altogether, our results suggest that the multisite specificity of the M. capricolum DusB enzyme could be an ancestral property.
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Affiliation(s)
- Bruno Faivre
- Laboratoire De Chimie Des Processus Biologiques, CNRS-UMR 8229, Collège De France, Sorbonne Université, UPMC Université. Paris 06, Paris, France
| | - Murielle Lombard
- Laboratoire De Chimie Des Processus Biologiques, CNRS-UMR 8229, Collège De France, Sorbonne Université, UPMC Université. Paris 06, Paris, France
| | - Soufyan Fakroun
- Sorbonne Université, IBPS, Biology of Aging and Adaptation, Paris, France
| | - Chau-Duy-Tam Vo
- Laboratoire De Chimie Des Processus Biologiques, CNRS-UMR 8229, Collège De France, Sorbonne Université, UPMC Université. Paris 06, Paris, France
| | | | - Vincent Guérineau
- Institue De Chimie De Substances Naturelles, Centre De Recherche De Gif CNRS, Gif-sur-Yvette, France
| | - Ludovic Pecqueur
- Laboratoire De Chimie Des Processus Biologiques, CNRS-UMR 8229, Collège De France, Sorbonne Université, UPMC Université. Paris 06, Paris, France
| | - Marc Fontecave
- Laboratoire De Chimie Des Processus Biologiques, CNRS-UMR 8229, Collège De France, Sorbonne Université, UPMC Université. Paris 06, Paris, France
| | - Valérie De Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA; University of Florida Genetics Institute, Gainesville, FL, USA
| | - Damien Brégeon
- Sorbonne Université, IBPS, Biology of Aging and Adaptation, Paris, France
| | - Djemel Hamdane
- Laboratoire De Chimie Des Processus Biologiques, CNRS-UMR 8229, Collège De France, Sorbonne Université, UPMC Université. Paris 06, Paris, France
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24
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Patel DT, O'Bier NS, Schuler EJA, Marconi RT. The Treponema denticola DgcA protein (TDE0125) is a functional diguanylate cyclase. Pathog Dis 2021; 79:6102550. [PMID: 33452878 DOI: 10.1093/femspd/ftab004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 01/13/2021] [Indexed: 11/12/2022] Open
Abstract
Periodontal disease (PD) is a progressive inflammatory condition characterized by degradation of the gingival epithelium, periodontal ligament, and alveolar bone ultimately resulting in tooth loss. Treponema denticola is a keystone periopathogen that contributes to immune dysregulation and direct tissue destruction. As periodontal disease develops, T. denticola must adapt to environmental, immunological and physiochemical changes in the subgingival crevice. Treponema denticola produces bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP), an important regulatory nucleotide. While T. denticola encodes several putative diguanylate cyclases (DGCs), none have been studied and hence the biological role of c-di-GMP in oral treponemes remains largely unexplored. Here, we demonstrate that the T. denticola open reading frame, TDE0125, encodes a functional DGC designated as DgcA (Diguanylate cyclase A). The dgcA gene is universal among T. denticola isolates, highly conserved and is a stand-alone GGEEF protein with a GAF domain. Recombinant DgcA converts GTP to c-di-GMP using either manganese or magnesium under aerobic and anaerobic reaction conditions. Size exclusion chromatography revealed that DgcA exists as a homodimer and in larger oligomers. Site-directed mutagenesis of residues that define the putative inhibitory site of DgcA suggest that c-di-GMP production is allosterically regulated. This report is the first to characterize a DGC of an oral treponeme.
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Affiliation(s)
- Dhara T Patel
- Department of Microbiology and Immunology, VCU Medical Center, 1112 East Clay Street, Room 101 McGuire Hall, PO Box 980678, Richmond, VA 23298-0678, USA
| | - Nathaniel S O'Bier
- Department of Microbiology and Immunology, VCU Medical Center, 1112 East Clay Street, Room 101 McGuire Hall, PO Box 980678, Richmond, VA 23298-0678, USA
| | - Edward J A Schuler
- Department of Microbiology and Immunology, VCU Medical Center, 1112 East Clay Street, Room 101 McGuire Hall, PO Box 980678, Richmond, VA 23298-0678, USA
| | - Richard T Marconi
- Department of Microbiology and Immunology, VCU Medical Center, 1112 East Clay Street, Room 101 McGuire Hall, PO Box 980678, Richmond, VA 23298-0678, USA
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25
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Yu J, Shinoda A, Kato K, Tanaka I, Yao M. A solution-free crystal-mounting platform for native SAD. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2020; 76:938-945. [PMID: 33021495 DOI: 10.1107/s2059798320011584] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 08/25/2020] [Indexed: 11/11/2022]
Abstract
The native SAD phasing method uses the anomalous scattering signals from the S atoms contained in most proteins, the P atoms in nucleic acids or other light atoms derived from the solution used for crystallization. These signals are very weak and careful data collection is required, which makes this method very difficult. One way to enhance the anomalous signal is to use long-wavelength X-rays; however, these wavelengths are more strongly absorbed by the materials in the pathway. Therefore, a crystal-mounting platform for native SAD data collection that removes solution around the crystals has been developed. This platform includes a novel solution-free mounting tool and an automatic robot, which extracts the surrounding solution, flash-cools the crystal and inserts the loop into a UniPuck cassette for use in the synchrotron. Eight protein structures (including two new structures) have been successfully solved by the native SAD method from crystals prepared using this platform.
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Affiliation(s)
- Jian Yu
- Faculty of Advanced Life Science, Hokkaido University, North 10 West 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
| | - Akira Shinoda
- Faculty of Advanced Life Science, Hokkaido University, North 10 West 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
| | - Koji Kato
- Faculty of Advanced Life Science, Hokkaido University, North 10 West 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
| | - Isao Tanaka
- Faculty of Advanced Life Science, Hokkaido University, North 10 West 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
| | - Min Yao
- Faculty of Advanced Life Science, Hokkaido University, North 10 West 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
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26
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Xu ZC, Feng PM, Yang H, Qiu WR, Chen W, Lin H. iRNAD: a computational tool for identifying D modification sites in RNA sequence. Bioinformatics 2020; 35:4922-4929. [PMID: 31077296 DOI: 10.1093/bioinformatics/btz358] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 03/01/2019] [Accepted: 04/27/2019] [Indexed: 12/19/2022] Open
Abstract
MOTIVATION Dihydrouridine (D) is a common RNA post-transcriptional modification found in eukaryotes, bacteria and a few archaea. The modification can promote the conformational flexibility of individual nucleotide bases. And its levels are increased in cancerous tissues. Therefore, it is necessary to detect D in RNA for further understanding its functional roles. Since wet-experimental techniques for the aim are time-consuming and laborious, it is urgent to develop computational models to identify D modification sites in RNA. RESULTS We constructed a predictor, called iRNAD, for identifying D modification sites in RNA sequence. In this predictor, the RNA samples derived from five species were encoded by nucleotide chemical property and nucleotide density. Support vector machine was utilized to perform the classification. The final model could produce the overall accuracy of 96.18% with the area under the receiver operating characteristic curve of 0.9839 in jackknife cross-validation test. Furthermore, we performed a series of validations from several aspects and demonstrated the robustness and reliability of the proposed model. AVAILABILITY AND IMPLEMENTATION A user-friendly web-server called iRNAD can be freely accessible at http://lin-group.cn/server/iRNAD, which will provide convenience and guide to users for further studying D modification.
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Affiliation(s)
- Zhao-Chun Xu
- Computer Department, Jingdezhen Ceramic Institute, Jingdezhen, China.,Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology and Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Peng-Mian Feng
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Hui Yang
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology and Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Wang-Ren Qiu
- Computer Department, Jingdezhen Ceramic Institute, Jingdezhen, China
| | - Wei Chen
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Hao Lin
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology and Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
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27
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Mathlin J, Le Pera L, Colombo T. A Census and Categorization Method of Epitranscriptomic Marks. Int J Mol Sci 2020; 21:ijms21134684. [PMID: 32630140 PMCID: PMC7370119 DOI: 10.3390/ijms21134684] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 06/26/2020] [Accepted: 06/27/2020] [Indexed: 12/21/2022] Open
Abstract
In the past few years, thorough investigation of chemical modifications operated in the cells on ribonucleic acid (RNA) molecules is gaining momentum. This new field of research has been dubbed “epitranscriptomics”, in analogy to best-known epigenomics, to stress the potential of ensembles of RNA modifications to constitute a post-transcriptional regulatory layer of gene expression orchestrated by writer, reader, and eraser RNA-binding proteins (RBPs). In fact, epitranscriptomics aims at identifying and characterizing all functionally relevant changes involving both non-substitutional chemical modifications and editing events made to the transcriptome. Indeed, several types of RNA modifications that impact gene expression have been reported so far in different species of cellular RNAs, including ribosomal RNAs, transfer RNAs, small nuclear RNAs, messenger RNAs, and long non-coding RNAs. Supporting functional relevance of this largely unknown regulatory mechanism, several human diseases have been associated directly to RNA modifications or to RBPs that may play as effectors of epitranscriptomic marks. However, an exhaustive epitranscriptome’s characterization, aimed to systematically classify all RNA modifications and clarify rules, actors, and outcomes of this promising regulatory code, is currently not available, mainly hampered by lack of suitable detecting technologies. This is an unfortunate limitation that, thanks to an unprecedented pace of technological advancements especially in the sequencing technology field, is likely to be overcome soon. Here, we review the current knowledge on epitranscriptomic marks and propose a categorization method based on the reference ribonucleotide and its rounds of modifications (“stages”) until reaching the given modified form. We believe that this classification scheme can be useful to coherently organize the expanding number of discovered RNA modifications.
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Affiliation(s)
- Julia Mathlin
- Department of Life Sciences and Medicine, University of Luxembourg, L-4367 Belvaux, Luxembourg
- Correspondence: (J.M.); (L.L.P.); Tel.: +39-06-4991-0556 (L.L.P.)
| | - Loredana Le Pera
- CNR-Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), 70126 Bari, Italy
- CNR-Institute of Molecular Biology and Pathology (IBPM), 00185 Rome, Italy;
- Correspondence: (J.M.); (L.L.P.); Tel.: +39-06-4991-0556 (L.L.P.)
| | - Teresa Colombo
- CNR-Institute of Molecular Biology and Pathology (IBPM), 00185 Rome, Italy;
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28
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Bou-Nader C, Barraud P, Pecqueur L, Pérez J, Velours C, Shepard W, Fontecave M, Tisné C, Hamdane D. Molecular basis for transfer RNA recognition by the double-stranded RNA-binding domain of human dihydrouridine synthase 2. Nucleic Acids Res 2019; 47:3117-3126. [PMID: 30605527 PMCID: PMC6451096 DOI: 10.1093/nar/gky1302] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 12/12/2018] [Accepted: 12/29/2018] [Indexed: 11/17/2022] Open
Abstract
Double stranded RNA-binding domain (dsRBD) is a ubiquitous domain specialized in the recognition of double-stranded RNAs (dsRNAs). Present in many proteins and enzymes involved in various functional roles of RNA metabolism, including RNA splicing, editing, and transport, dsRBD generally binds to RNAs that lack complex structures. However, this belief has recently been challenged by the discovery of a dsRBD serving as a major tRNA binding module for human dihydrouridine synthase 2 (hDus2), a flavoenzyme that catalyzes synthesis of dihydrouridine within the complex elbow structure of tRNA. We here unveil the molecular mechanism by which hDus2 dsRBD recognizes a tRNA ligand. By solving the crystal structure of this dsRBD in complex with a dsRNA together with extensive characterizations of its interaction with tRNA using mutagenesis, NMR and SAXS, we establish that while hDus2 dsRBD retains a conventional dsRNA recognition capability, the presence of an N-terminal extension appended to the canonical domain provides additional residues for binding tRNA in a structure-specific mode of action. Our results support that this extension represents a feature by which the dsRBD specializes in tRNA biology and more broadly highlight the importance of structural appendages to canonical domains in promoting the emergence of functional diversity.
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Affiliation(s)
- Charles Bou-Nader
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et Marie Curie, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Pierre Barraud
- Institut de biologie physico-chimique (IBPC), CNRS, UMR 8261 CNRS/Université Paris Diderot, 13 rue Pierre et Marie Curie, Paris 75005, France.,Laboratoire de cristallographie et RMN biologiques, UMR 8015, CNRS, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Ludovic Pecqueur
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et Marie Curie, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Javier Pérez
- Synchrotron Soleil, L'Orme des Merisiers, BP 48, 91192 Gif sur Yvette Cedex, France
| | - Christophe Velours
- Macromolecular interaction platform of I2BC, UMR9198, Centre de Recherche de Gif-sur-Yvette, France
| | - William Shepard
- Synchrotron Soleil, L'Orme des Merisiers, BP 48, 91192 Gif sur Yvette Cedex, France
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et Marie Curie, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Carine Tisné
- Institut de biologie physico-chimique (IBPC), CNRS, UMR 8261 CNRS/Université Paris Diderot, 13 rue Pierre et Marie Curie, Paris 75005, France.,Laboratoire de cristallographie et RMN biologiques, UMR 8015, CNRS, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Djemel Hamdane
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et Marie Curie, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
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29
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Abstract
Ribonucleic acid (RNA) is involved in translation and transcription, which are the mechanisms in which cells express genes (Alberts et al., 2002). The three classes of RNA discussed are transfer RNA (tRNA), messenger RNA (mRNA), and ribosomal RNA (rRNA). mRNA is the transcript encoded from DNA, rRNA is associated with ribosomes, and tRNA is associated with amino acids and is used to read mRNA transcripts to make proteins (Lodish, Berk, Zipursky, et al., 2000). Interestingly, the function of tRNA, rRNA, and mRNA can be significantly altered by chemical modifications at the co-transcriptional and post-transcriptional levels, and there are over 171 of these modifications identified thus far (Boccaletto et al., 2018; Modomics-Modified bases, 2017). Several of these modifications are linked to diseases such as cancer, diabetes, and neurological disorders. In this review, we will introduce a few RNA modifications with biological functions and how dysregulation of these RNA modifications is linked to human disease.
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Affiliation(s)
- Amber Yanas
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Kathy Fange Liu
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.
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30
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Bou-Nader C, Pecqueur L, Barraud P, Fontecave M, Tisné C, Sacquin-Mora S, Hamdane D. Conformational Stability Adaptation of a Double-Stranded RNA-Binding Domain to Transfer RNA Ligand. Biochemistry 2019; 58:2463-2473. [PMID: 31045345 DOI: 10.1021/acs.biochem.9b00111] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The double-stranded RNA-binding domain (dsRBD) is a broadly distributed domain among RNA-maturing enzymes. Although this domain recognizes dsRNA's structures via a conserved canonical structure adopting an α1-β1β2β3-α2 topology, several dsRBDs can accommodate discrete structural extensions expanding further their functional repertoire. How these structural elements engage cooperative communications with the canonical structure and how they contribute to the dsRBD's overall folding are poorly understood. Here, we addressed these issues using the dsRBD of human dihydrouridine synthase-2 (hDus2) (hDus2-dsRBD) as a model. This dsRBD harbors N- and C-terminal extensions, the former being directly involved in the recognition of tRNA substrate of hDus2. These extensions engage residues that form a long-range hydrophobic network (LHN) outside the RNA-binding interface. We show by coarse-grain Brownian dynamics that the Nt-extension and its residues F359 and Y364 rigidify the major folding nucleus of the canonical structure via an indirect effect. hDus2-dsRBD unfolds following a two-state cooperative model, whereas both F359A and Y364A mutants, designed to destabilize this LHN, unfold irreversibly. Structural and computational analyses show that these mutants are unstable due to an increase in the dynamics of the two extensions favoring solvent exposure of α2-helix and weakening the main folding nucleus rigidity. This LHN appears essential for maintaining a thermodynamic stability of the overall system and eventually a functional conformation for tRNA recognition. Altogether, our findings suggest that functional adaptability of extended dsRBDs is promoted by a cooperative hydrophobic coupling between the extensions acting as effectors and the folding nucleus of the canonical structure.
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Affiliation(s)
- Charles Bou-Nader
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France , Université Pierre et Marie Curie , 11 place Marcelin Berthelot , 75231 Paris Cedex 05 , France
| | - Ludovic Pecqueur
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France , Université Pierre et Marie Curie , 11 place Marcelin Berthelot , 75231 Paris Cedex 05 , France
| | - Pierre Barraud
- Expression Génétique Microbienne , UMR 8261, CNRS, Université Paris, Institut de Biologie Physico-Chimique , 13 rue Pierre et Marie Curie , 75005 Paris , France
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France , Université Pierre et Marie Curie , 11 place Marcelin Berthelot , 75231 Paris Cedex 05 , France
| | - Carine Tisné
- Expression Génétique Microbienne , UMR 8261, CNRS, Université Paris, Institut de Biologie Physico-Chimique , 13 rue Pierre et Marie Curie , 75005 Paris , France
| | - Sophie Sacquin-Mora
- Laboratoire de Biochimie Théorique, CNRS UPR9080 , Institut de Biologie Physico-Chimique , 13 rue Pierre et Marie Curie , 75005 Paris , France
| | - Djemel Hamdane
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France , Université Pierre et Marie Curie , 11 place Marcelin Berthelot , 75231 Paris Cedex 05 , France
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31
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Hori H. Regulatory Factors for tRNA Modifications in Extreme- Thermophilic Bacterium Thermus thermophilus. Front Genet 2019; 10:204. [PMID: 30906314 PMCID: PMC6418473 DOI: 10.3389/fgene.2019.00204] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 02/26/2019] [Indexed: 01/02/2023] Open
Abstract
Thermus thermophilus is an extreme-thermophilic bacterium that can grow at a wide range of temperatures (50-83°C). To enable T. thermophilus to grow at high temperatures, several biomolecules including tRNA and tRNA modification enzymes show extreme heat-resistance. Therefore, the modified nucleosides in tRNA from T. thermophilus have been studied mainly from the view point of tRNA stabilization at high temperatures. Such studies have shown that several modifications stabilize the structure of tRNA and are essential for survival of the organism at high temperatures. Together with tRNA modification enzymes, the modified nucleosides form a network that regulates the extent of different tRNA modifications at various temperatures. In this review, I describe this network, as well as the tRNA recognition mechanism of individual tRNA modification enzymes. Furthermore, I summarize the roles of other tRNA stabilization factors such as polyamines and metal ions.
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Affiliation(s)
- Hiroyuki Hori
- Department of Materials Sciences and Biotechnology, Graduate School of Science and Engineering, Ehime University, Matsuyama, Japan
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32
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Identification of D Modification Sites by Integrating Heterogeneous Features in Saccharomyces cerevisiae. Molecules 2019; 24:molecules24030380. [PMID: 30678171 PMCID: PMC6384727 DOI: 10.3390/molecules24030380] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 12/17/2018] [Accepted: 12/17/2018] [Indexed: 11/16/2022] Open
Abstract
As an abundant post-transcriptional modification, dihydrouridine (D) has been found in transfer RNA (tRNA) from bacteria, eukaryotes, and archaea. Nonetheless, knowledge of the exact biochemical roles of dihydrouridine in mediating tRNA function is still limited. Accurate identification of the position of D sites is essential for understanding their functions. Therefore, it is desirable to develop novel methods to identify D sites. In this study, an ensemble classifier was proposed for the detection of D modification sites in the Saccharomyces cerevisiae transcriptome by using heterogeneous features. The jackknife test results demonstrate that the proposed predictor is promising for the identification of D modification sites. It is anticipated that the proposed method can be widely used for identifying D modification sites in tRNA.
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33
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Hori H, Kawamura T, Awai T, Ochi A, Yamagami R, Tomikawa C, Hirata A. Transfer RNA Modification Enzymes from Thermophiles and Their Modified Nucleosides in tRNA. Microorganisms 2018; 6:E110. [PMID: 30347855 PMCID: PMC6313347 DOI: 10.3390/microorganisms6040110] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 10/17/2018] [Accepted: 10/17/2018] [Indexed: 12/11/2022] Open
Abstract
To date, numerous modified nucleosides in tRNA as well as tRNA modification enzymes have been identified not only in thermophiles but also in mesophiles. Because most modified nucleosides in tRNA from thermophiles are common to those in tRNA from mesophiles, they are considered to work essentially in steps of protein synthesis at high temperatures. At high temperatures, the structure of unmodified tRNA will be disrupted. Therefore, thermophiles must possess strategies to stabilize tRNA structures. To this end, several thermophile-specific modified nucleosides in tRNA have been identified. Other factors such as RNA-binding proteins and polyamines contribute to the stability of tRNA at high temperatures. Thermus thermophilus, which is an extreme-thermophilic eubacterium, can adapt its protein synthesis system in response to temperature changes via the network of modified nucleosides in tRNA and tRNA modification enzymes. Notably, tRNA modification enzymes from thermophiles are very stable. Therefore, they have been utilized for biochemical and structural studies. In the future, thermostable tRNA modification enzymes may be useful as biotechnology tools and may be utilized for medical science.
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Affiliation(s)
- Hiroyuki Hori
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Takuya Kawamura
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Takako Awai
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Anna Ochi
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Ryota Yamagami
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Chie Tomikawa
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Akira Hirata
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
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34
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Bou-Nader C, Brégeon D, Pecqueur L, Fontecave M, Hamdane D. Electrostatic Potential in the tRNA Binding Evolution of Dihydrouridine Synthases. Biochemistry 2018; 57:5407-5414. [DOI: 10.1021/acs.biochem.8b00584] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Charles Bou-Nader
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, 11 place Marcelin Berthelot, Paris 75231 Cedex 05, France
| | - Damien Brégeon
- CNRS, IBPS, Biology of Aging and Adaptation, Sorbonne Université, 7 quai Saint Bernard, Paris 7525 Cedex 05, France
| | - Ludovic Pecqueur
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, 11 place Marcelin Berthelot, Paris 75231 Cedex 05, France
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, 11 place Marcelin Berthelot, Paris 75231 Cedex 05, France
| | - Djemel Hamdane
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, 11 place Marcelin Berthelot, Paris 75231 Cedex 05, France
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Bou-Nader C, Montémont H, Guérineau V, Jean-Jean O, Brégeon D, Hamdane D. Unveiling structural and functional divergences of bacterial tRNA dihydrouridine synthases: perspectives on the evolution scenario. Nucleic Acids Res 2018; 46:1386-1394. [PMID: 29294097 PMCID: PMC5814906 DOI: 10.1093/nar/gkx1294] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 12/12/2017] [Accepted: 12/18/2017] [Indexed: 12/22/2022] Open
Abstract
Post-transcriptional base modifications are important to the maturation process of transfer RNAs (tRNAs). Certain modifications are abundant and present at several positions in tRNA as for example the dihydrouridine, a modified base found in the three domains of life. Even though the function of dihydrourine is not well understood, its high content in tRNAs from psychrophilic bacteria or cancer cells obviously emphasizes a central role in cell adaptation. The reduction of uridine to dihydrouridine is catalyzed by a large family of flavoenzymes named dihydrouridine synthases (Dus). Prokaryotes have three Dus (A, B and C) wherein DusB is considered as an ancestral protein from which the two others derived via gene duplications. Here, we unequivocally established the complete substrate specificities of the three Escherichia coli Dus and solved the crystal structure of DusB, enabling for the first time an exhaustive structural comparison between these bacterial flavoenzymes. Based on our results, we propose an evolutionary scenario explaining how substrate specificities has been diversified from a single structural fold.
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Affiliation(s)
- Charles Bou-Nader
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Hugo Montémont
- Sorbonne Universités, UPMC University, Paris 06, IBPS, UMR8256, Biology of Aging and Adaptation, 7 quai Saint Bernard, 75252 Paris Cedex 05, France
| | - Vincent Guérineau
- Institue de Chimie de Substances Naturelles, Centre de Recherche de Gif CNRS, 1 avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Olivier Jean-Jean
- Sorbonne Universités, UPMC University, Paris 06, IBPS, UMR8256, Biology of Aging and Adaptation, 7 quai Saint Bernard, 75252 Paris Cedex 05, France
| | - Damien Brégeon
- Sorbonne Universités, UPMC University, Paris 06, IBPS, UMR8256, Biology of Aging and Adaptation, 7 quai Saint Bernard, 75252 Paris Cedex 05, France
| | - Djemel Hamdane
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
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37
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Lorenz C, Lünse CE, Mörl M. tRNA Modifications: Impact on Structure and Thermal Adaptation. Biomolecules 2017; 7:E35. [PMID: 28375166 PMCID: PMC5485724 DOI: 10.3390/biom7020035] [Citation(s) in RCA: 216] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 03/27/2017] [Accepted: 03/28/2017] [Indexed: 12/27/2022] Open
Abstract
Transfer RNAs (tRNAs) are central players in translation, functioning as adapter molecules between the informational level of nucleic acids and the functional level of proteins. They show a highly conserved secondary and tertiary structure and the highest density of post-transcriptional modifications among all RNAs. These modifications concentrate in two hotspots-the anticodon loop and the tRNA core region, where the D- and T-loop interact with each other, stabilizing the overall structure of the molecule. These modifications can cause large rearrangements as well as local fine-tuning in the 3D structure of a tRNA. The highly conserved tRNA shape is crucial for the interaction with a variety of proteins and other RNA molecules, but also needs a certain flexibility for a correct interplay. In this context, it was shown that tRNA modifications are important for temperature adaptation in thermophilic as well as psychrophilic organisms, as they modulate rigidity and flexibility of the transcripts, respectively. Here, we give an overview on the impact of modifications on tRNA structure and their importance in thermal adaptation.
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Affiliation(s)
- Christian Lorenz
- Institute of Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany.
| | - Christina E Lünse
- Institute of Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany.
| | - Mario Mörl
- Institute of Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany.
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38
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McKenney KM, Alfonzo JD. From Prebiotics to Probiotics: The Evolution and Functions of tRNA Modifications. Life (Basel) 2016; 6:E13. [PMID: 26985907 PMCID: PMC4810244 DOI: 10.3390/life6010013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 02/27/2016] [Accepted: 03/07/2016] [Indexed: 12/13/2022] Open
Abstract
All nucleic acids in cells are subject to post-transcriptional chemical modifications. These are catalyzed by a myriad of enzymes with exquisite specificity and that utilize an often-exotic array of chemical substrates. In no molecule are modifications more prevalent than in transfer RNAs. In the present document, we will attempt to take a chemical rollercoaster ride from prebiotic times to the present, with nucleoside modifications as key players and tRNA as the centerpiece that drove the evolution of biological systems to where we are today. These ideas will be put forth while touching on several examples of tRNA modification enzymes and their modus operandi in cells. In passing, we submit that the choice of tRNA is not a whimsical one but rather highlights its critical function as an essential invention for the evolution of protein enzymes.
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Affiliation(s)
- Katherine M McKenney
- The Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA.
| | - Juan D Alfonzo
- The Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA.
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.
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Dyubankova N, Sochacka E, Kraszewska K, Nawrot B, Herdewijn P, Lescrinier E. Contribution of dihydrouridine in folding of the D-arm in tRNA. Org Biomol Chem 2015; 13:4960-6. [PMID: 25815904 DOI: 10.1039/c5ob00164a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Posttranscriptional modifications of transfer RNAs (tRNAs) are proven to be critical for all core aspects of tRNA function. While the majority of tRNA modifications were discovered in the 1970s, their contribution in tRNA folding, stability, and decoding often remains elusive. In this work an NMR study was performed to obtain more insight in the role of the dihydrouridine (D) modification in the D-arm of tRNAi(Met) from S. pombe. While the unmodified oligonucleotide adopted several undefined conformations that interconvert in solution, the presence of a D nucleoside triggered folding into a hairpin with a stable stem and flexible loop region. Apparently the D modification is required in the studied sequence to fold into a stable hairpin. Therefore we conclude that D contributes to the correct folding and stability of D-arm in tRNA. In contrast to what is generally assumed for nucleic acids, the sharp 'imino' signal for the D nucleobase at 10 ppm in 90% H2O is not indicative for the presence of a stable hydrogen bond. The strong increase in pKa upon loss of the aromatic character in the modified nucleobase slows down the exchange of its 'imino' proton significantly, allowing its observation even in an isolated D nucleoside in 90% H2O in acidic to neutral conditions.
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Affiliation(s)
- N Dyubankova
- Medicinal Chemistry, Department of Pharmaceutical Sciences, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium.
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Nomura Y, Ohno S, Nishikawa K, Yokogawa T. Correlation between the stability of tRNA tertiary structure and the catalytic efficiency of a tRNA-modifying enzyme, archaeal tRNA-guanine transglycosylase. Genes Cells 2015; 21:41-52. [PMID: 26663416 DOI: 10.1111/gtc.12317] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 10/22/2015] [Indexed: 11/29/2022]
Abstract
In many archaeal tRNAs, archaeosine is found at position 15. During archaeosine biosynthesis, archaeal tRNA-guanine transglycosylase (ArcTGT) first replaces the guanine base at position 15 with 7-cyano-7-deazaguanine (preQ0). In this study, we investigated whether modified nucleosides in tRNA substrates would affect ArcTGT incorporation of preQ0. We prepared a series of hypomodified tRNAs(Ser)(GGA) from Escherichia coli strains lacking each tRNA-modifying enzyme. Measurement of ArcTGT kinetic parameters with the various tRNAs(Ser)(GGA) as substrates showed that the Km decreased due to the lack of modified nucleosides. The tRNAs(Ser)(GGA) melting profiles resulted in experimental evidence showing that each modified nucleoside in tRNA(Ser)(GGA) enhanced tRNA stability. Furthermore, the ArcTGT K(m) strongly correlated with the melting temperature (T(m)), suggesting that the unstable tRNA containing fewer modified nucleosides served as a better ArcTGT substrate. These results show that preQ0 incorporation into tRNA by ArcTGT takes place early in the archaeal tRNA modification process.
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Affiliation(s)
- Yuichiro Nomura
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
| | - Satoshi Ohno
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
| | - Kazuya Nishikawa
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
| | - Takashi Yokogawa
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
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Bou-Nader C, Pecqueur L, Bregeon D, Kamah A, Guérineau V, Golinelli-Pimpaneau B, Guimarães BG, Fontecave M, Hamdane D. An extended dsRBD is required for post-transcriptional modification in human tRNAs. Nucleic Acids Res 2015; 43:9446-56. [PMID: 26429968 PMCID: PMC4627097 DOI: 10.1093/nar/gkv989] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 09/19/2015] [Indexed: 12/25/2022] Open
Abstract
In tRNA, dihydrouridine is a conserved modified base generated by the post-transcriptional reduction of uridine. Formation of dihydrouridine 20, located in the D-loop, is catalyzed by dihydrouridine synthase 2 (Dus2). Human Dus2 (HsDus2) expression is upregulated in lung cancers, offering a growth advantage throughout its ability to interact with components of the translation apparatus and inhibit apoptosis. Here, we report the crystal structure of the individual domains of HsDus2 and their functional characterization. HsDus2 is organized into three major modules. The N-terminal catalytic domain contains the flavin cofactor involved in the reduction of uridine. The second module is the conserved α-helical domain known as the tRNA binding domain in HsDus2 homologues. It is connected via a flexible linker to an unusual extended version of a dsRNA binding domain (dsRBD). Enzymatic assays and yeast complementation showed that the catalytic domain binds selectively NADPH but cannot reduce uridine in the absence of the dsRBD. While in Dus enzymes from bacteria, plants and fungi, tRNA binding is essentially achieved by the α-helical domain, we showed that in HsDus2 this function is carried out by the dsRBD. This is the first reported case of a tRNA-modifying enzyme carrying a dsRBD used to bind tRNAs.
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Affiliation(s)
- Charles Bou-Nader
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, France, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Ludovic Pecqueur
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, France, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Damien Bregeon
- Sorbonne Universités, UPMC Univ. Paris 06, IBPS, UMR8256, Biology of Aging and Adaptation, F-75005 Paris, France
| | - Amina Kamah
- Université de Lille-Nord de France, CNRS UMR 8576, Institut Fédératif de Recherches 147, Villeneuve d'Ascq, France
| | - Vincent Guérineau
- Institut de Chimie des Substances Naturelles, Centre de Recherche de Gif, CNRS, 1 avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Béatrice Golinelli-Pimpaneau
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, France, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Beatriz G Guimarães
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, 91190 Gif-sur-Yvette, France
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, France, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Djemel Hamdane
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, France, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
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Whelan F, Jenkins HT, Griffiths SC, Byrne RT, Dodson EJ, Antson AA. From bacterial to human dihydrouridine synthase: automated structure determination. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:1564-71. [PMID: 26143927 PMCID: PMC4498606 DOI: 10.1107/s1399004715009220] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 05/14/2015] [Indexed: 11/10/2022]
Abstract
The reduction of uridine to dihydrouridine at specific positions in tRNA is catalysed by dihydrouridine synthase (Dus) enzymes. Increased expression of human dihydrouridine synthase 2 (hDus2) has been linked to pulmonary carcinogenesis, while its knockdown decreased cancer cell line viability, suggesting that it may serve as a valuable target for therapeutic intervention. Here, the X-ray crystal structure of a construct of hDus2 encompassing the catalytic and tRNA-recognition domains (residues 1-340) determined at 1.9 Å resolution is presented. It is shown that the structure can be determined automatically by phenix.mr_rosetta starting from a bacterial Dus enzyme with only 18% sequence identity and a significantly divergent structure. The overall fold of the human Dus2 is similar to that of bacterial enzymes, but has a larger recognition domain and a unique three-stranded antiparallel β-sheet insertion into the catalytic domain that packs next to the recognition domain, contributing to domain-domain interactions. The structure may inform the development of novel therapeutic approaches in the fight against lung cancer.
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Affiliation(s)
- Fiona Whelan
- Department of Biology, The University of York, Heslington, York YO10 5DD, England
| | - Huw T. Jenkins
- York Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York YO10 5DD, England
| | - Samuel C. Griffiths
- Division of Structural Biology, University of Oxford, Headington, Oxford OX3 7BN, England
| | - Robert T. Byrne
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-University Munich, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Eleanor J. Dodson
- York Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York YO10 5DD, England
| | - Alfred A. Antson
- York Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York YO10 5DD, England
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43
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Kusuba H, Yoshida T, Iwasaki E, Awai T, Kazayama A, Hirata A, Tomikawa C, Yamagami R, Hori H. In vitrodihydrouridine formation by tRNA dihydrouridine synthase fromThermus thermophilus, an extreme-thermophilic eubacterium. J Biochem 2015; 158:513-21. [DOI: 10.1093/jb/mvv066] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 05/30/2015] [Indexed: 01/08/2023] Open
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Byrne RT, Jenkins HT, Peters DT, Whelan F, Stowell J, Aziz N, Kasatsky P, Rodnina MV, Koonin EV, Konevega AL, Antson AA. Major reorientation of tRNA substrates defines specificity of dihydrouridine synthases. Proc Natl Acad Sci U S A 2015; 112:6033-7. [PMID: 25902496 PMCID: PMC4434734 DOI: 10.1073/pnas.1500161112] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The reduction of specific uridines to dihydrouridine is one of the most common modifications in tRNA. Increased levels of the dihydrouridine modification are associated with cancer. Dihydrouridine synthases (Dus) from different subfamilies selectively reduce distinct uridines, located at spatially unique positions of folded tRNA, into dihydrouridine. Because the catalytic center of all Dus enzymes is conserved, it is unclear how the same protein fold can be reprogrammed to ensure that nucleotides exposed at spatially distinct faces of tRNA can be accommodated in the same active site. We show that the Escherichia coli DusC is specific toward U16 of tRNA. Unexpectedly, crystal structures of DusC complexes with tRNA(Phe) and tRNA(Trp) show that Dus subfamilies that selectively modify U16 or U20 in tRNA adopt identical folds but bind their respective tRNA substrates in an almost reverse orientation that differs by a 160° rotation. The tRNA docking orientation appears to be guided by subfamily-specific clusters of amino acids ("binding signatures") together with differences in the shape of the positively charged tRNA-binding surfaces. tRNA orientations are further constrained by positional differences between the C-terminal "recognition" domains. The exquisite substrate specificity of Dus enzymes is therefore controlled by a relatively simple mechanism involving major reorientation of the whole tRNA molecule. Such reprogramming of the enzymatic specificity appears to be a unique evolutionary solution for altering tRNA recognition by the same protein fold.
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Affiliation(s)
- Robert T Byrne
- York Structural Biology Laboratory, Department of Chemistry, and
| | - Huw T Jenkins
- York Structural Biology Laboratory, Department of Chemistry, and
| | - Daniel T Peters
- York Structural Biology Laboratory, Department of Chemistry, and
| | - Fiona Whelan
- York Structural Biology Laboratory, Department of Chemistry, and
| | - James Stowell
- York Structural Biology Laboratory, Department of Chemistry, and Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - Naveed Aziz
- Department of Biology, University of York, York, YO10 5DD, United Kingdom; Genome Canada, Ottawa, ON K2P 1P1, Canada
| | - Pavel Kasatsky
- Molecular and Radiation Biophysics Department, B.P. Konstantinov Petersburg Nuclear Physics Institute of National Research Centre "Kurchatov Institute," 188300 Gatchina, Russia; St. Petersburg State Polytechnic University, 195251 St. Petersburg, Russia
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany; and
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894
| | - Andrey L Konevega
- Molecular and Radiation Biophysics Department, B.P. Konstantinov Petersburg Nuclear Physics Institute of National Research Centre "Kurchatov Institute," 188300 Gatchina, Russia; St. Petersburg State Polytechnic University, 195251 St. Petersburg, Russia; Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany; and
| | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, and
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45
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Farrugia DN, Elbourne LDH, Mabbutt BC, Paulsen IT. A novel family of integrases associated with prophages and genomic islands integrated within the tRNA-dihydrouridine synthase A (dusA) gene. Nucleic Acids Res 2015; 43:4547-57. [PMID: 25883135 PMCID: PMC4482086 DOI: 10.1093/nar/gkv337] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 04/01/2015] [Indexed: 12/12/2022] Open
Abstract
Genomic islands play a key role in prokaryotic genome plasticity. Genomic islands integrate into chromosomal loci such as transfer RNA genes and protein coding genes, whilst retaining various cargo genes that potentially bestow novel functions on the host organism. A gene encoding a putative integrase was identified at a single site within the 5′ end of the dusA gene in the genomes of over 200 bacteria. This integrase was discovered to be a component of numerous genomic islands, which appear to share a target site within the dusA gene. dusA encodes the tRNA-dihydrouridine synthase A enzyme, which catalyses the post-transcriptional reduction of uridine to dihydrouridine in tRNA. Genomic islands encoding homologous dusA-associated integrases were found at a much lower frequency within the related dusB and dusC genes, and non-dus genes. Excision of these dusA-associated islands from the chromosome as circularized intermediates was confirmed by polymerase chain reaction. Analysis of the dusA-associated islands indicated that they were highly diverse, with the integrase gene representing the only universal common feature.
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Affiliation(s)
- Daniel N Farrugia
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Liam D H Elbourne
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Bridget C Mabbutt
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Ian T Paulsen
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
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Hamdane D, Guelorget A, Guérineau V, Golinelli-Pimpaneau B. Dynamics of RNA modification by a multi-site-specific tRNA methyltransferase. Nucleic Acids Res 2014; 42:11697-706. [PMID: 25217588 PMCID: PMC4191401 DOI: 10.1093/nar/gku820] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In most organisms, the widely conserved 1-methyl-adenosine58 (m1A58) tRNA modification is catalyzed by an S-adenosyl-L-methionine (SAM)-dependent, site-specific enzyme TrmI. In archaea, TrmI also methylates the adjacent adenine 57, m1A57 being an obligatory intermediate of 1-methyl-inosine57 formation. To study this multi-site specificity, we used three oligoribonucleotide substrates of Pyrococcus abyssi TrmI (PabTrmI) containing a fluorescent 2-aminopurine (2-AP) at the two target positions and followed the RNA binding kinetics and methylation reactions by stopped-flow and mass spectrometry. PabTrmI did not modify 2-AP but methylated the adjacent target adenine. 2-AP seriously impaired the methylation of A57 but not A58, confirming that PabTrmI methylates efficiently the first adenine of the A57A58A59 sequence. PabTrmI binding provoked a rapid increase of fluorescence, attributed to base unstacking in the environment of 2-AP. Then, a slow decrease was observed only with 2-AP at position 57 and SAM, suggesting that m1A58 formation triggers RNA release. A model of the protein-tRNA complex shows both target adenines in proximity of SAM and emphasizes no major tRNA conformational change except base flipping during the reaction. The solvent accessibility of the SAM pocket is not affected by the tRNA, thereby enabling S-adenosyl-L-homocysteine to be replaced by SAM without prior release of monomethylated tRNA.
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Affiliation(s)
- Djemel Hamdane
- Laboratoire d'Enzymologie et Biochimie Structurales, Centre de Recherche de Gif, CNRS, 1 avenue de la Terrasse, 91198 Gif-sur-Yvette, France Laboratoire de Chimie des Processus Biologiques, Collège de France, CNRS, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Amandine Guelorget
- Laboratoire d'Enzymologie et Biochimie Structurales, Centre de Recherche de Gif, CNRS, 1 avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Vincent Guérineau
- Institut de Chimie des Substances Naturelles, Centre de Recherche de Gif, CNRS, 1 avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Béatrice Golinelli-Pimpaneau
- Laboratoire d'Enzymologie et Biochimie Structurales, Centre de Recherche de Gif, CNRS, 1 avenue de la Terrasse, 91198 Gif-sur-Yvette, France Laboratoire de Chimie des Processus Biologiques, Collège de France, CNRS, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
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Mishanina TV, Corcoran JM, Kohen A. Substrate activation in flavin-dependent thymidylate synthase. J Am Chem Soc 2014; 136:10597-600. [PMID: 25025487 PMCID: PMC4121000 DOI: 10.1021/ja506108b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Thymidylate is a critical DNA nucleotide
that has to be synthesized
in cells de novo by all organisms. Flavin-dependent
thymidylate synthase (FDTS) catalyzes the final step in this de novo production of thymidylate in many human pathogens,
but it is absent from humans. The FDTS reaction proceeds via a chemical
route that is different from its human enzyme analogue, making FDTS
a potential antimicrobial target. The chemical mechanism of FDTS is
still not understood, and the two most recently proposed mechanisms
involve reaction intermediates that are unusual in pyrimidine biosynthesis
and biology in general. These mechanisms differ in the relative timing
of the reaction of the flavin with the substrate. The consequence
of this difference is significant: the intermediates are cationic
in one case and neutral in the other, an important consideration in
the construction of mechanism-based enzyme inhibitors. Here we test
these mechanisms via chemical trapping of reaction intermediates,
stopped-flow, and substrate hydrogen isotope exchange techniques.
Our findings suggest that an initial activation of the pyrimidine
substrate by reduced flavin is required for catalysis, and a revised
mechanism is proposed on the basis of previous and new data. These
findings and the newly proposed mechanism add an important piece to
the puzzle of the mechanism of FDTS and suggest a new class of intermediates
that, in the future, may serve as targets for mechanism-based design
of FDTS-specific inhibitors.
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Affiliation(s)
- Tatiana V Mishanina
- Department of Chemistry, University of Iowa , Iowa City, Iowa 52242-1727, United States
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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.
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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
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Ritson DJ, Sutherland JD. Conversion of biosynthetic precursors of RNA to those of DNA by photoredox chemistry. J Mol Evol 2014; 78:245-50. [PMID: 24736972 PMCID: PMC4037592 DOI: 10.1007/s00239-014-9617-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 03/20/2014] [Indexed: 11/29/2022]
Abstract
Soon after the origin of RNA-based life, depletion of prebiotically synthesised ribonucleotides would have driven the evolution of a biosynthetic pathway to these key building blocks. Ribozyme-catalysed nucleosidation-the key biosynthetic step-requires that ribose and the nucleobases are produced by abiotic chemistry and are relatively stable to the conditions of their synthesis. The most plausible prebiotic synthesis of sugars involves photoreduction of cyanohydrins by hydrogen sulphide in the presence of copper(I) cyanide, and we therefore subjected ribose to these conditions whereupon it was partially converted to 2-deoxyribose. Furthermore, a derivative of uracil is reduced under similar conditions to thymine. Thus, DNA biosynthetic precursors can be formed abiotically from those of RNA allowing for an early evolutionary transition to life based on RNA and DNA.
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Affiliation(s)
- Dougal J Ritson
- MRC-Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK,
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Chen M, Yu J, Tanaka Y, Tanaka M, Tanaka I, Yao M. Structure of dihydrouridine synthase C (DusC) from Escherichia coli. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:834-8. [PMID: 23908023 PMCID: PMC3729154 DOI: 10.1107/s1744309113019489] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 07/15/2013] [Indexed: 05/14/2023]
Abstract
Dihydrouridine (D) is one of the most widely conserved tRNA modifications. Dihydrouridine synthase (Dus) is responsible for introducing D modifications into RNA by the reduction of uridine. Recently, a unique substrate-recognition mechanism using a small adapter molecule has been proposed for Thermus thermophilus Dus (TthDusC). To acquire insight regarding its substrate-recognition mechanism, the crystal structure of DusC from Escherichia coli (EcoDusC) was determined at 2.1 Å resolution. EcoDusC was shown to be composed of two domains: an N-terminal catalytic domain and a C-terminal tRNA-binding domain. An L-shaped electron density surrounded by highly conserved residues was found in the active site, as observed for TthDus. Structure comparison with TthDus indicated that the N-terminal region has a similar structure, whereas the C-terminal domain has marked differences in its relative orientation to the N-terminal domain as well as in its own structure. These observations suggested that Dus proteins adopt a common substrate-recognition mechanism using an adapter molecule, whereas the manner of tRNA binding is diverse.
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Affiliation(s)
- Minghao Chen
- Graduate School of Life Sciences, Hokkaido University, Sapporo 060-0810, Japan
| | - Jian Yu
- Faculty of Advanced Life Sciences, Hokkaido University, Sapporo 060-0810, Japan
| | - Yoshikazu Tanaka
- Faculty of Advanced Life Sciences, Hokkaido University, Sapporo 060-0810, Japan
| | - Miyuki Tanaka
- Faculty of Advanced Life Sciences, Hokkaido University, Sapporo 060-0810, Japan
| | - Isao Tanaka
- Faculty of Advanced Life Sciences, Hokkaido University, Sapporo 060-0810, Japan
| | - Min Yao
- Faculty of Advanced Life Sciences, Hokkaido University, Sapporo 060-0810, Japan
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