1
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Yared MJ, Marcelot A, Barraud P. Beyond the Anticodon: tRNA Core Modifications and Their Impact on Structure, Translation and Stress Adaptation. Genes (Basel) 2024; 15:374. [PMID: 38540433 PMCID: PMC10969862 DOI: 10.3390/genes15030374] [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: 02/21/2024] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 06/14/2024] Open
Abstract
Transfer RNAs (tRNAs) are heavily decorated with post-transcriptional chemical modifications. Approximately 100 different modifications have been identified in tRNAs, and each tRNA typically contains 5-15 modifications that are incorporated at specific sites along the tRNA sequence. These modifications may be classified into two groups according to their position in the three-dimensional tRNA structure, i.e., modifications in the tRNA core and modifications in the anticodon-loop (ACL) region. Since many modified nucleotides in the tRNA core are involved in the formation of tertiary interactions implicated in tRNA folding, these modifications are key to tRNA stability and resistance to RNA decay pathways. In comparison to the extensively studied ACL modifications, tRNA core modifications have generally received less attention, although they have been shown to play important roles beyond tRNA stability. Here, we review and place in perspective selected data on tRNA core modifications. We present their impact on tRNA structure and stability and report how these changes manifest themselves at the functional level in translation, fitness and stress adaptation.
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Affiliation(s)
| | | | - Pierre Barraud
- Expression Génétique Microbienne, Université Paris Cité, CNRS, Institut de Biologie Physico-Chimique, F-75005 Paris, France; (M.-J.Y.); (A.M.)
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2
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Rodgers MT, Seidu YS, Israel E. Influence of 2'-Modifications (O-Methylation, Fluorination, and Stereochemical Inversion) on the Base Pairing Energies of Protonated Cytidine Nucleoside Analogue Base Pairs: Implications for the Stabilities of i-Motif Structures. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023. [PMID: 37294839 DOI: 10.1021/jasms.3c00108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Naturally occurring and chemically engineered modifications are among the most powerful strategies explored for fine-tuning the conformational characteristics and intrinsic stability of nucleic acids topologies. Modifications at the 2'-position of the ribose or 2'-deoxyribose moieties differentiate nucleic acid structures and have a significant impact on their electronic properties and base-pairing interactions. 2'-O-Methylation, a common post-transcriptional modification of tRNA, is directly involved in modulating specific anticodon-codon base-pairing interactions. 2'-Fluorinated and arabino nucleosides possess novel and beneficial medicinal properties and find use as therapeutics for treating viral diseases and cancer. However, the potential to deploy 2'-modified cytidine chemistries for tuning i-motif stability is largely unknown. To address this knowledge gap, the effects of 2'-modifications including O-methylation, fluorination, and stereochemical inversion on the base-pairing interactions of protonated cytidine nucleoside analogue base pairs, the core stabilizing interactions of i-motif structures, are examined using complementary threshold collision-induced dissociation techniques and computational methods. The 2'-modified cytidine nucleoside analogues investigated here include 2'-O-methylcytidine, 2'-fluoro-2'-deoxycytidine, arabinofuranosylcytosine, 2'-fluoro-arabinofuranosylcytosine, and 2',2'-difluoro-2'-deoxycytidine. All five 2'-modifications examined here are found to enhance the base-pairing interactions relative to the canonical DNA and RNA cytidine nucleosides with the greatest enhancements arising from 2'-O-methylation and 2',2'-difluorination, suggesting that these modifications should well be tolerated in the narrow grooves of i-motif conformations.
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Affiliation(s)
- M T Rodgers
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Yakubu S Seidu
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - E Israel
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
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3
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Sarkar AK, Sarzynska J, Lahiri A. Ensemble Allosteric Model for the Modified Wobble Hypothesis. J Phys Chem Lett 2020; 11:6337-6343. [PMID: 32701298 DOI: 10.1021/acs.jpclett.0c00854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The residue 2-thiouridine (s2U) provides a remarkable example for the "modified wobble" hypothesis, which postulates that some post-transcriptional modifications at the wobble position of tRNAs restrict recognition of degenerate codons. Through extensive molecular dynamics simulations using our χIDRP force field parameters, we demonstrate how this modification shifts the conformational ensemble from a predominantly disordered, as in the case of an RNA pentamer (GUUUC), to a substantially ordered population in Gs2UUUC. Our simulations clearly showed that the van der Waals interaction of sulfur played a major role in driving the disorder-to-order transition. The conformational redistribution and the slowing down of the transition between the clusters within the population in the presence of s2U suggest ensemble allostery to be a key mechanism that may play a general role in the functioning of the wobble modifications of tRNAs.
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Affiliation(s)
- Aditya K Sarkar
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata 700 009, India
| | - Joanna Sarzynska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Ansuman Lahiri
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata 700 009, India
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4
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Ong AAL, Toh DFK, Krishna MS, Patil KM, Okamura K, Chen G. Incorporating 2-Thiouracil into Short Double-Stranded RNA-Binding Peptide Nucleic Acids for Enhanced Recognition of A-U Pairs and for Targeting a MicroRNA Hairpin Precursor. Biochemistry 2019; 58:3444-3453. [PMID: 31318532 DOI: 10.1021/acs.biochem.9b00521] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Chemically modified short peptide nucleic acids (PNAs) recognize RNA duplexes under near physiological conditions by major-groove PNA·RNA-RNA triplex formation and show great promise for the development of RNA-targeting probes and therapeutics. Thymine (T) and uracil (U) are often incorporated into PNAs to recognize A-U pairs through major-groove T·A-U and U·A-U base triple formation. Incorporation of a modified nucleobase, 2-thiouracil (s2U), into triplex-forming oligonucleotides stabilizes both DNA and RNA triplexes. Thiolation of uracil causes a decrease in the dehydration energy penalty for triplex formation as well as a decrease in the pKa of the N3 atom, which may result in improved hydrogen bonding in addition to enhanced base stacking interactions, similar to the previously reported thiolation effect of pseudoisocytosine (J to L substitution). Here, we incorporated s2U into short PNAs, followed by binding studies of a series of s2U-modified PNAs. We demonstrated by nondenaturing polyacrylamide gel electrophoresis and thermal melting experiments that s2U and L incorporated into dsRNA-binding PNAs (dbPNAs) enhance the recognition of A-U and G-C pairs, respectively, in RNA duplexes in a position-independent manner, with no appreciable binding to the DNA duplex. Combining s2U and L modifications in dbPNAs facilitates enhanced recognition of dsRNAs and maintains selective binding to dsRNAs over ssRNAs. We further demonstrated through a cell-free assay the application of the s2U- and L-modified dbPNAs (8-mer, with a molecular mass of ∼2.3 kDa) in the inhibition of the pre-microRNA-198 maturation in a substrate-specific manner. Thus, s2U-modified dbPNAs may be generally useful for the enhanced and selective recognition of RNA duplexes and for the regulation of RNA functions.
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Affiliation(s)
- Alan Ann Lerk Ong
- NTU Institute for Health Technologies (HeathTech NTU), Interdisciplinary Graduate School , Nanyang Technological University , 50 Nanyang Drive , Singapore 637553.,Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Desiree-Faye Kaixin Toh
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Manchugondanahalli S Krishna
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Kiran M Patil
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Katsutomo Okamura
- Division of Biological Sciences , Nara Institute of Science and Technology , 8916-5 Takayama , Ikoma , Nara 630-0192 , Japan
| | - Gang Chen
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
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5
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The emerging impact of tRNA modifications in the brain and nervous system. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:412-428. [PMID: 30529455 DOI: 10.1016/j.bbagrm.2018.11.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 11/21/2018] [Accepted: 11/23/2018] [Indexed: 01/19/2023]
Abstract
A remarkable number of neurodevelopmental disorders have been linked to defects in tRNA modifications. These discoveries place tRNA modifications in the spotlight as critical modulators of gene expression pathways that are required for proper organismal growth and development. Here, we discuss the emerging molecular and cellular functions of the diverse tRNA modifications linked to cognitive and neurological disorders. In particular, we describe how the structure and location of a tRNA modification influences tRNA folding, stability, and function. We then highlight how modifications in tRNA can impact multiple aspects of protein translation that are instrumental for maintaining proper cellular proteostasis. Importantly, we describe how perturbations in tRNA modification lead to a spectrum of deleterious biological outcomes that can disturb neurodevelopment and neurological function. Finally, we summarize the biological themes shared by the different tRNA modifications linked to cognitive disorders and offer insight into the future questions that remain to decipher the role of tRNA modifications. This article is part of a Special Issue entitled: mRNA modifications in gene expression control edited by Dr. Soller Matthias and Dr. Fray Rupert.
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6
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Koh CS, Sarin LP. Transfer RNA modification and infection – Implications for pathogenicity and host responses. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1861:419-432. [DOI: 10.1016/j.bbagrm.2018.01.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/04/2018] [Accepted: 01/19/2018] [Indexed: 12/19/2022]
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7
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Sochacka E, Lodyga-Chruscinska E, Pawlak J, Cypryk M, Bartos P, Ebenryter-Olbinska K, Leszczynska G, Nawrot B. C5-substituents of uridines and 2-thiouridines present at the wobble position of tRNA determine the formation of their keto-enol or zwitterionic forms - a factor important for accuracy of reading of guanosine at the 3΄-end of the mRNA codons. Nucleic Acids Res 2017; 45:4825-4836. [PMID: 28088758 PMCID: PMC5416851 DOI: 10.1093/nar/gkw1347] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 12/30/2016] [Indexed: 12/19/2022] Open
Abstract
Modified nucleosides present in the wobble position of the tRNA anticodons regulate protein translation through tuning the reading of mRNA codons. Among 40 of such nucleosides, there are modified uridines containing either a sulfur atom at the C2 position and/or a substituent at the C5 position of the nucleobase ring. It is already evidenced that tRNAs with 2-thiouridines at the wobble position preferentially read NNA codons, while the reading mode of the NNG codons by R5U/R5S2U-containing anticodons is still elusive. For a series of 18 modified uridines and 2-thiouridines, we determined the pKa values and demonstrated that both modifying elements alter the electron density of the uracil ring and modulate the acidity of their N3H proton. In aqueous solutions at physiological pH the 2-thiouridines containing aminoalkyl C5-substituents are ionized in ca. 50%. The results, confirmed also by theoretical calculations, indicate that the preferential binding of the modified units bearing non-ionizable 5-substituents to guanosine in the NNG codons may obey the alternative C-G-like (Watson–Crick) mode, while binding of those bearing aminoalkyl C5-substituents (protonated under physiological conditions) and especially those with a sulfur atom at the C2 position, adopt a zwitterionic form and interact with guanosine via a ‘new wobble’ pattern.
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Affiliation(s)
- Elzbieta Sochacka
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Elzbieta Lodyga-Chruscinska
- Institute of General Food Chemistry, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Justyna Pawlak
- Institute of General Food Chemistry, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Marek Cypryk
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Paulina Bartos
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Katarzyna Ebenryter-Olbinska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland.,Department of Computer Modeling, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Grazyna Leszczynska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Barbara Nawrot
- Department of Computer Modeling, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
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8
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Väre VYP, Eruysal ER, Narendran A, Sarachan KL, Agris PF. Chemical and Conformational Diversity of Modified Nucleosides Affects tRNA Structure and Function. Biomolecules 2017; 7:E29. [PMID: 28300792 PMCID: PMC5372741 DOI: 10.3390/biom7010029] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 03/06/2017] [Accepted: 03/06/2017] [Indexed: 12/21/2022] Open
Abstract
RNAs are central to all gene expression through the control of protein synthesis. Four major nucleosides, adenosine, guanosine, cytidine and uridine, compose RNAs and provide sequence variation, but are limited in contributions to structural variation as well as distinct chemical properties. The ability of RNAs to play multiple roles in cellular metabolism is made possible by extensive variation in length, conformational dynamics, and the over 100 post-transcriptional modifications. There are several reviews of the biochemical pathways leading to RNA modification, but the physicochemical nature of modified nucleosides and how they facilitate RNA function is of keen interest, particularly with regard to the contributions of modified nucleosides. Transfer RNAs (tRNAs) are the most extensively modified RNAs. The diversity of modifications provide versatility to the chemical and structural environments. The added chemistry, conformation and dynamics of modified nucleosides occurring at the termini of stems in tRNA's cloverleaf secondary structure affect the global three-dimensional conformation, produce unique recognition determinants for macromolecules to recognize tRNAs, and affect the accurate and efficient decoding ability of tRNAs. This review will discuss the impact of specific chemical moieties on the structure, stability, electrochemical properties, and function of tRNAs.
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Affiliation(s)
- Ville Y P Väre
- The RNA Institute, Departments of Biological Sciences and Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA.
| | - Emily R Eruysal
- The RNA Institute, Departments of Biological Sciences and Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA.
| | - Amithi Narendran
- The RNA Institute, Departments of Biological Sciences and Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA.
| | - Kathryn L Sarachan
- The RNA Institute, Departments of Biological Sciences and Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA.
| | - Paul F Agris
- The RNA Institute, Departments of Biological Sciences and Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA.
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9
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Abstract
Wobble uridines (U34) are generally modified in all species. U34 modifications can be essential in metazoans but are not required for viability in fungi. In this review, we provide an overview on the types of modifications and how they affect the physico-chemical properties of wobble uridines. We describe the molecular machinery required to introduce these modifications into tRNA posttranscriptionally and discuss how posttranslational regulation may affect the activity of the modifying enzymes. We highlight the activity of anticodon specific RNases that target U34 containing tRNA. Finally, we discuss how defects in wobble uridine modifications lead to phenotypes in different species. Importantly, this review will mainly focus on the cytoplasmic tRNAs of eukaryotes. A recent review has extensively covered their bacterial and mitochondrial counterparts.1
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Affiliation(s)
- Raffael Schaffrath
- a Institut für Biologie, FG Mikrobiologie , Universität Kassel , Germany
| | - Sebastian A Leidel
- b Max Planck Institute for Molecular Biomedicine , Germany.,c Cells-in-Motion Cluster of Excellence , University of Münster , Münster , Germany.,d Medical Faculty , University of Münster , Albert-Schweitzer-Campus 1, Münster , Germany
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10
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Jaroensuk J, Atichartpongkul S, Chionh YH, Wong YH, Liew CW, McBee ME, Thongdee N, Prestwich EG, DeMott MS, Mongkolsuk S, Dedon PC, Lescar J, Fuangthong M. Methylation at position 32 of tRNA catalyzed by TrmJ alters oxidative stress response in Pseudomonas aeruginosa. Nucleic Acids Res 2016; 44:10834-10848. [PMID: 27683218 PMCID: PMC5159551 DOI: 10.1093/nar/gkw870] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 09/17/2016] [Accepted: 09/20/2016] [Indexed: 02/04/2023] Open
Abstract
Bacteria respond to environmental stresses using a variety of signaling and gene expression pathways, with translational mechanisms being the least well understood. Here, we identified a tRNA methyltransferase in Pseudomonas aeruginosa PA14, trmJ, which confers resistance to oxidative stress. Analysis of tRNA from a trmJ mutant revealed that TrmJ catalyzes formation of Cm, Um, and, unexpectedly, Am. Defined in vitro analyses revealed that tRNAMet(CAU) and tRNATrp(CCA) are substrates for Cm formation, tRNAGln(UUG), tRNAPro(UGG), tRNAPro(CGG) and tRNAHis(GUG) for Um, and tRNAPro(GGG) for Am. tRNASer(UGA), previously observed as a TrmJ substrate in Escherichia coli, was not modified by PA14 TrmJ. Position 32 was confirmed as the TrmJ target for Am in tRNAPro(GGG) and Um in tRNAGln(UUG) by mass spectrometric analysis. Crystal structures of the free catalytic N-terminal domain of TrmJ show a 2-fold symmetrical dimer with an active site located at the interface between the monomers and a flexible basic loop positioned to bind tRNA, with conformational changes upon binding of the SAM-analog sinefungin. The loss of TrmJ rendered PA14 sensitive to H2O2 exposure, with reduced expression of oxyR-recG, katB-ankB, and katE. These results reveal that TrmJ is a tRNA:Cm32/Um32/Am32 methyltransferase involved in translational fidelity and the oxidative stress response.
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Affiliation(s)
- Juthamas Jaroensuk
- Applied Biological Sciences Program, Chulabhorn Graduate Institute, Bangkok, Thailand.,Singapore-MIT Alliance for Research and Technology, Singapore
| | | | - Yok Hian Chionh
- Singapore-MIT Alliance for Research and Technology, Singapore
| | - Yee Hwa Wong
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Chong Wai Liew
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore
| | - Megan E McBee
- Singapore-MIT Alliance for Research and Technology, Singapore
| | - Narumon Thongdee
- Applied Biological Sciences Program, Chulabhorn Graduate Institute, Bangkok, Thailand
| | - Erin G Prestwich
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Michael S DeMott
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Skorn Mongkolsuk
- Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand.,Department of Biotechnology, Faculty of Sciences, Mahidol University, Bangkok, Thailand.,Center of Excellence on Environmental Health and Toxicology (EHT), Bangkok, Thailand
| | - Peter C Dedon
- Singapore-MIT Alliance for Research and Technology, Singapore .,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Julien Lescar
- School of Biological Sciences, Nanyang Technological University, Singapore .,NTU Institute of Structural Biology, Nanyang Technological University, Singapore.,UPMC UMRS CR7 - CNRS ERL 8255-INSERM U1135 Centre d' Immunologie et des Maladies Infectieuses, Paris, France
| | - Mayuree Fuangthong
- Applied Biological Sciences Program, Chulabhorn Graduate Institute, Bangkok, Thailand .,Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand.,Center of Excellence on Environmental Health and Toxicology (EHT), Bangkok, Thailand
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11
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Duechler M, Leszczyńska G, Sochacka E, Nawrot B. Nucleoside modifications in the regulation of gene expression: focus on tRNA. Cell Mol Life Sci 2016; 73:3075-95. [PMID: 27094388 PMCID: PMC4951516 DOI: 10.1007/s00018-016-2217-y] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 03/25/2016] [Accepted: 04/04/2016] [Indexed: 01/10/2023]
Abstract
Both, DNA and RNA nucleoside modifications contribute to the complex multi-level regulation of gene expression. Modified bases in tRNAs modulate protein translation rates in a highly dynamic manner. Synonymous codons, which differ by the third nucleoside in the triplet but code for the same amino acid, may be utilized at different rates according to codon-anticodon affinity. Nucleoside modifications in the tRNA anticodon loop can favor the interaction with selected codons by stabilizing specific base pairs. Similarly, weakening of base pairing can discriminate against binding to near-cognate codons. mRNAs enriched in favored codons are translated in higher rates constituting a fine-tuning mechanism for protein synthesis. This so-called codon bias establishes a basic protein level, but sometimes it is necessary to further adjust the production rate of a particular protein to actual requirements, brought by, e.g., stages in circadian rhythms, cell cycle progression or exposure to stress. Such an adjustment is realized by the dynamic change of tRNA modifications resulting in the preferential translation of mRNAs coding for example for stress proteins to facilitate cell survival. Furthermore, tRNAs contribute in an entirely different way to another, less specific stress response consisting in modification-dependent tRNA cleavage that contributes to the general down-regulation of protein synthesis. In this review, we summarize control functions of nucleoside modifications in gene regulation with a focus on recent findings on protein synthesis control by tRNA base modifications.
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Affiliation(s)
- Markus Duechler
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Lodz, Poland.
| | - Grażyna Leszczyńska
- Institute of Organic Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Lodz, Poland
| | - Elzbieta Sochacka
- Institute of Organic Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Lodz, Poland
| | - Barbara Nawrot
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Lodz, Poland
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12
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13
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Abstract
Transfer RNA (tRNA) from all organisms on this planet contains modified nucleosides, which are derivatives of the four major nucleosides. tRNA from Escherichia coli/Salmonella enterica contains 31 different modified nucleosides, which are all, except for one (Queuosine[Q]), synthesized on an oligonucleotide precursor, which through specific enzymes later matures into tRNA. The corresponding structural genes for these enzymes are found in mono- and polycistronic operons, the latter of which have a complex transcription and translation pattern. The syntheses of some of them (e.g.,several methylated derivatives) are catalyzed by one enzyme, which is position and base specific, but synthesis of some have a very complex biosynthetic pathway involving several enzymes (e.g., 2-thiouridines, N6-threonyladenosine [t6A],and Q). Several of the modified nucleosides are essential for viability (e.g.,lysidin, t6A, 1-methylguanosine), whereas deficiency in others induces severe growth defects. However, some have no or only a small effect on growth at laboratory conditions. Modified nucleosides that are present in the anticodon loop or stem have a fundamental influence on the efficiency of charging the tRNA, reading cognate codons, and preventing missense and frameshift errors. Those, which are present in the body of the tRNA, have a primarily stabilizing effect on the tRNA. Thus, the ubiquitouspresence of these modified nucleosides plays a pivotal role in the function of the tRNA by their influence on the stability and activity of the tRNA.
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14
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Bartos P, Ebenryter-Olbinska K, Sochacka E, Nawrot B. The influence of the C5 substituent on the 2-thiouridine desulfuration pathway and the conformational analysis of the resulting 4-pyrimidinone products. Bioorg Med Chem 2015; 23:5587-94. [DOI: 10.1016/j.bmc.2015.07.030] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 07/14/2015] [Accepted: 07/15/2015] [Indexed: 11/29/2022]
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15
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Chwialkowska A, Wielgus E, Leszczynska G, Sobczak M, Mikolajczyk B, Sochacka E, Nawrot B. An efficient approach for conversion of 5-substituted 2-thiouridines built in RNA oligomers into corresponding desulfured 4-pyrimidinone products. Bioorg Med Chem Lett 2015; 25:3100-4. [PMID: 26112441 DOI: 10.1016/j.bmcl.2015.06.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 06/03/2015] [Accepted: 06/05/2015] [Indexed: 01/09/2023]
Abstract
An efficient approach for the desulfuration of C5-substituted 2-thiouridines (R5S2U) bound in the RNA chain exclusively to 4-pyrimidinone nucleoside (R5H2U)-containing RNA products is proposed. This post-synthetic transformation avoids the preparation of a suitably protected H2U phosphoramidite, which otherwise would be necessary for solid-phase synthesis of the modified RNA. Optimization of the desulfuration, which included reaction stoichiometry, time and temperature, allowed to transform a set of ten R5S2U-RNAs into their R5H2U-RNA congeners in ca. 90% yield.
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Affiliation(s)
- Anna Chwialkowska
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Ewelina Wielgus
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Grazyna Leszczynska
- Institute of Organic Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Milena Sobczak
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Barbara Mikolajczyk
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Elzbieta Sochacka
- Institute of Organic Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Barbara Nawrot
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland.
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16
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Sochacka E, Szczepanowski RH, Cypryk M, Sobczak M, Janicka M, Kraszewska K, Bartos P, Chwialkowska A, Nawrot B. 2-Thiouracil deprived of thiocarbonyl function preferentially base pairs with guanine rather than adenine in RNA and DNA duplexes. Nucleic Acids Res 2015; 43:2499-512. [PMID: 25690900 PMCID: PMC4357714 DOI: 10.1093/nar/gkv109] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 01/30/2015] [Accepted: 02/02/2015] [Indexed: 12/12/2022] Open
Abstract
2-Thiouracil-containing nucleosides are essential modified units of natural and synthetic nucleic acids. In particular, the 5-substituted-2-thiouridines (S2Us) present in tRNA play an important role in tuning the translation process through codon-anticodon interactions. The enhanced thermodynamic stability of S2U-containing RNA duplexes and the preferred S2U-A versus S2U-G base pairing are appreciated characteristics of S2U-modified molecular probes. Recently, we have demonstrated that 2-thiouridine (alone or within an RNA chain) is predominantly transformed under oxidative stress conditions to 4-pyrimidinone riboside (H2U) and not to uridine. Due to the important biological functions and various biotechnological applications for sulfur-containing nucleic acids, we compared the thermodynamic stabilities of duplexes containing desulfured products with those of 2-thiouracil-modified RNA and DNA duplexes. Differential scanning calorimetry experiments and theoretical calculations demonstrate that upon 2-thiouracil desulfuration to 4-pyrimidinone, the preferred base pairing of S2U with adenosine is lost, with preferred base pairing with guanosine observed instead. Therefore, biological processes and in vitro assays in which oxidative desulfuration of 2-thiouracil-containing components occurs may be altered. Moreover, we propose that the H2U-G base pair is a suitable model for investigation of the preferred recognition of 3'-G-ending versus A-ending codons by tRNA wobble nucleosides, which may adopt a 4-pyrimidinone-type structural motif.
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Affiliation(s)
- Elzbieta Sochacka
- Institute of Organic Chemistry, Technical University of Lodz, Zeromskiego 116, 90-924 Lodz, Poland
| | - Roman H Szczepanowski
- International Institute of Molecular and Cell Biology, Ks. J. Trojdena 4, 02-109 Warsaw, Poland
| | - Marek Cypryk
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Milena Sobczak
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Magdalena Janicka
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Karina Kraszewska
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Paulina Bartos
- Institute of Organic Chemistry, Technical University of Lodz, Zeromskiego 116, 90-924 Lodz, Poland
| | - Anna Chwialkowska
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Barbara Nawrot
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
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17
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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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18
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Sochacka E, Bartos P, Kraszewska K, Nawrot B. Desulfuration of 2-thiouridine with hydrogen peroxide in the physiological pH range 6.6–7.6 is pH-dependent and results in two distinct products. Bioorg Med Chem Lett 2013; 23:5803-5. [DOI: 10.1016/j.bmcl.2013.08.114] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 08/29/2013] [Accepted: 08/30/2013] [Indexed: 10/26/2022]
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19
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Zhou Y, Kierzek E, Loo ZP, Antonio M, Yau YH, Chuah YW, Geifman-Shochat S, Kierzek R, Chen G. Recognition of RNA duplexes by chemically modified triplex-forming oligonucleotides. Nucleic Acids Res 2013; 41:6664-73. [PMID: 23658228 PMCID: PMC3711454 DOI: 10.1093/nar/gkt352] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Triplex is emerging as an important RNA tertiary structure motif, in which consecutive non-canonical base pairs form between a duplex and a third strand. RNA duplex region is also often functionally important site for protein binding. Thus, triplex-forming oligonucleotides (TFOs) may be developed to regulate various biological functions involving RNA, such as viral ribosomal frameshifting and reverse transcription. How chemical modification in TFOs affects RNA triplex stability, however, is not well understood. Here, we incorporated locked nucleic acid, 2-thio U- and 2′-O methyl-modified residues in a series of all pyrimidine RNA TFOs, and we studied the binding to two RNA hairpin structures. The 12-base-triple major-groove pyrimidine–purine–pyrimidine triplex structures form between the duplex regions of RNA/DNA hairpins and the complementary RNA TFOs. Ultraviolet-absorbance-detected thermal melting studies reveal that the locked nucleic acid and 2-thio U modifications in TFOs strongly enhance triplex formation with both parental RNA and DNA duplex regions. In addition, we found that incorporation of 2′-O methyl-modified residues in a TFO destabilizes and stabilizes triplex formation with RNA and DNA duplex regions, respectively. The (de)stabilization of RNA triplex formation may be facilitated through modulation of van der Waals contact, base stacking, hydrogen bonding, backbone pre-organization, geometric compatibility and/or dehydration energy. Better understanding of the molecular determinants of RNA triplex structure stability lays the foundation for designing and discovering novel sequence-specific duplex-binding ligands as diagnostic and therapeutic agents targeting RNA.
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Affiliation(s)
- Yuan Zhou
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore
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20
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Insight into reaction mechanism and product formation a C8-purine radical in RNA: a theoretical perspective. Theor Chem Acc 2013. [DOI: 10.1007/s00214-013-1355-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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21
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Nawrot B, Sochacka E, Düchler M. tRNA structural and functional changes induced by oxidative stress. Cell Mol Life Sci 2011; 68:4023-32. [PMID: 21833586 PMCID: PMC3221842 DOI: 10.1007/s00018-011-0773-8] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Revised: 07/04/2011] [Accepted: 07/07/2011] [Indexed: 11/29/2022]
Abstract
Oxidatively damaged biomolecules impair cellular functions and contribute to the pathology of a variety of diseases. RNA is also attacked by reactive oxygen species, and oxidized RNA is increasingly recognized as an important contributor to neurodegenerative complications in humans. Recently, evidence has accumulated supporting the notion that tRNA is involved in cellular responses to various stress conditions. This review focuses on the intriguing consequences of oxidative modification of tRNA at the structural and functional level.
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Affiliation(s)
- Barbara Nawrot
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, 112, Sienkiewicza Street, 90-363 Lodz, Poland
| | - Elzbieta Sochacka
- Institute of Organic Chemistry, Technical University of Lodz, Zeromskiego 116, 90-924 Lodz, Poland
| | - Markus Düchler
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, 112, Sienkiewicza Street, 90-363 Lodz, Poland
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22
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Kraszewska K, Kaczyńska I, Jankowski S, Karolak-Wojciechowska J, Sochacka E. Desulfurization of 2-thiouracil nucleosides: conformational studies of 4-pyrimidinone nucleosides. Bioorg Med Chem 2011; 19:2443-9. [PMID: 21396827 DOI: 10.1016/j.bmc.2011.02.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Accepted: 02/03/2011] [Indexed: 10/18/2022]
Abstract
4-Pyrimidinone ribofuranoside (H(2)o(4)U) and 4-pyrimidinone 2'-deoxyribofuranoside (dH(2)o(4)U) were synthesized by the oxidative desulfurization of parent 2-thiouracil nucleosides with m-chloroperbenzoic acid. The crystal structures of H(2)o(4)U and dH(2)o(4)U and their conformations in solution were determined and compared with corresponding 2-thiouracil and uracil nucleosides. The absence of a large 2-thiocarbonyl/2-carbonyl group in the nucleobase moiety results in C2'-endo puckering of the ribofuranose ring (S conformer) in the crystal structure of H(2)o(4)U, which is not typical of RNA nucleosides. Interestingly, the hydrogen bonding network in the crystals of dH(2)o(4)U stabilizes the sugar moiety conformation in the C3'-endo form (N conformer), rarely found in DNA nucleosides. In aqueous solution, dH(2)o(4)U reveals a similar population of the C2'-endo conformation (65%) to that of 2'-deoxy-2-thiouridine (62%), while the 62% population of the S conformer for H(2)o(4)U is significantly different from that of the parent 2-thiouridine, for which the N conformer is dominant (71%). Such a difference may be of biological importance, as the desulfurization process of natural tRNA 2-thiouridines may occur under conditions of oxidative stress in the cell and may influence the decoding process.
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Affiliation(s)
- Karina Kraszewska
- Institute of Organic Chemistry, Technical University of Lodz, Zeromskiego 116, 90-924 Lodz, Poland
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23
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Sochacka E, Kraszewska K, Sochacki M, Sobczak M, Janicka M, Nawrot B. The 2-thiouridine unit in the RNA strand is desulfured predominantly to 4-pyrimidinone nucleoside under in vitro oxidative stress conditions. Chem Commun (Camb) 2011; 47:4914-6. [DOI: 10.1039/c1cc10973a] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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24
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Abstract
Post-transcriptional ribonucleotide modification is a phenomenon best studied in tRNA, where it occurs most frequently and in great chemical diversity. This paper reviews the intrinsic network of modifications in the structural core of the tRNA, which governs structural flexibility and rigidity to fine-tune the molecule to peak performance and to regulate its steady-state level. Structural effects of RNA modifications range from nanometer-scale rearrangements to subtle restrictions of conformational space on the angstrom scale. Structural stabilization resulting from nucleotide modification results in increased thermal stability and translates into protection against unspecific degradation by bases and nucleases. Several mechanisms of specific degradation of hypomodified tRNA, which were only recently discovered, provide a link between structural and metabolic stability.
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Affiliation(s)
- Yuri Motorin
- Laboratoire ARN-RNP Maturation-Structure-Fonction, Enzymologie Moléculaire et Structurale (AREMS), UMR 7214 CNRS-UHP Faculté des Sciences et Techniques, Université Henri Poincaré, Nancy 1, Bld des Aiguillettes, BP 70239, 54506 Vandoeuvre-les-Nancy, France
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25
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Zhang RB, Eriksson LA. Theoretical study on conformational preferences of ribose in 2-thiouridine--the role of the 2'OH group. Phys Chem Chem Phys 2010; 12:3690-7. [PMID: 20358065 DOI: 10.1039/b921646d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Conformational changes in ribose are well-known to play a significant role in biomolecular identification. The mechanism of selectivity towards C3'-endo conformation (conformer b) in ribose of 2-thiouridine has been studied using DFT (B3LYP) and MP2 methodology, together with 6-31+G(d,p) basis set. The polarity of the C2S2 bond is enhanced due to the orientation of H2' towards the S2 atoms, which leads to a difference in the corresponding bond lengths, the atomic charges and the vO2'H2' stretch vibrations in all the conformers. NBO analysis shows that charge transfer mainly occurs in the C2N3 and C2S2 orbitals. The higher stability of conformer b is attributed to its larger orbital interaction energies within the 2-thiouracil base, and total orbital interaction energies of conformer b. Our conclusion is that the distant electrostatic rather than hydrogen bonding effects between 2'OH and the S2 atoms play the dominant role in the orbital interaction, and enhance the selectivity towards the C3'-endo conformation of ribose.
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Affiliation(s)
- Ru bo Zhang
- Institute for Chemical Physics, School of Science, Beijing Institute of Technology, Beijing 100081, China
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26
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Okamoto I, Cao S, Tanaka H, Seio K, Sekine M. Synthesis of 4-Thiopseudoisocytidine and 4-Thiopseudouridine as Components of Triplex-forming Oligonucleotides. CHEM LETT 2009. [DOI: 10.1246/cl.2009.174] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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27
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Okamoto I, Seio K, Sekine M. Study of the base discrimination ability of DNA and 2'-O-methylated RNA oligomers containing 2-thiouracil bases towards complementary RNA or DNA strands and their application to single base mismatch detection. Bioorg Med Chem 2008; 16:6034-41. [PMID: 18487052 DOI: 10.1016/j.bmc.2008.04.053] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2008] [Revised: 04/21/2008] [Accepted: 04/22/2008] [Indexed: 11/26/2022]
Abstract
Precise detection of target DNA and RNA sequences using chemically modified oligonucleotides is of crucial importance in gene analysis and gene silence. The hybridisation and base discrimination abilities of oligonucleotides containing 2'-O-methyl-2-thiouridine (s(2)Um) in homo- and hetero-duplexes composed of DNA and RNA strands have been studied in detail. When s(2)Um was incorporated into RNA or DNA strands, the hybridisation and base discrimination abilities of the modified RNA or DNA oligomers towards the complementary RNA strands were superior to those of the corresponding unmodified oligomers. On the other hand, their base discrimination abilities towards complementary DNA strands were almost the same as those of the unmodified ones. The base discrimination abilities of 2-thiouracil base-containing oligonucleotide probes on slide glass plates were also studied. These modified probes exhibited efficient detection of mismatched base pairing.
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Affiliation(s)
- Itaru Okamoto
- Department of Life Science, Tokyo Institute of Technology, Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
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28
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Okamoto I, Seio K, Sekine M. Triplex forming ability of oligonucleotides containing 2'-O-methyl-2-thiouridine or 2-thiothymidine. Bioorg Med Chem Lett 2006; 16:3334-6. [PMID: 16631365 DOI: 10.1016/j.bmcl.2006.02.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2005] [Revised: 02/08/2006] [Accepted: 02/09/2006] [Indexed: 11/24/2022]
Abstract
The triplex forming ability of oligonucleotides containing 2'-O-methyl-2-thiouridine (s2Um) and 2-thiothymidine (s2T) was studied. The UV melting experiments revealed that triplex forming oligonucleotides (TFOs) containing both s2Um or s2T stabilized significantly parallel triplexes. The main reason for stabilization of triplexes was due to the stacking effect of the 2-thiocarbonyl group. Moreover, it turned out that these modified TFOs had a high selectivity in recognition of a matched Hoogsteen base from a mismatched one.
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Affiliation(s)
- Itaru Okamoto
- Department of Life Science, Tokyo Institute of Technology, Japan
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29
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Okamoto I, Shohda KI, Seio K, Sekine M. Incorporation of 2′-O-Methyl-2-thiouridine into Oligoribonucleotides Induced Stable A-form Structure. CHEM LETT 2006. [DOI: 10.1246/cl.2006.136] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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30
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Okamoto I, Seio K, Sekine M. Improved synthesis of oligonucleotides containing 2-thiouridine derivatives by use of diluted iodine solution. Tetrahedron Lett 2006. [DOI: 10.1016/j.tetlet.2005.11.044] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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31
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Sochacka E, Frątczak I. Efficient desulfurization of 2-thiopyrimidine nucleosides to the corresponding 4-pyrimidinone analogues using trans-2-(phenylsulfonyl)-3-phenyloxaziridine. Tetrahedron Lett 2004. [DOI: 10.1016/j.tetlet.2004.07.052] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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32
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Okamoto I, Shohda KI, Seio K, Sekine M. A new route to 2'-O-alkyl-2-thiouridine derivatives via 4-O-protection of the uracil base and hybridization properties of oligonucleotides incorporating these modified nucleoside derivatives. J Org Chem 2004; 68:9971-82. [PMID: 14682690 DOI: 10.1021/jo035246b] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Oligonucleotides containing 2-thiouridine (s2U) in place of uridine form stable RNA duplexes with complementary RNAs. Particularly, this modified nucleoside has proved to recognize highly selectively adenosine, the genuine partner, without formation of a mismatched base pair with the guanosine counterpart. In this paper, we describe new methods for the synthesis of 2-thiouridine and various 2'-O-alkyl-2-thiouridine derivatives. Oligoribonucleotides having these modified nucleoside derivatives were synthesized, and their hybridization and structural properties were studied in detail by the 1H NMR analysis of these modified nucleosides and Tm experiments of RNA duplexes with their complementary RNA strands.
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Affiliation(s)
- Itaru Okamoto
- Department of Life Science and Frontier Collaborative Research Center, Tokyo Institute of Technology, Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
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33
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Hara-Yokoyama M, Yokoyama S, Watanabe T, Watanabe K, Kitazume M, Mitamura Y, Morii T, Takahashi S, Kuchino Y, Nishimura S, Miyazawa T. Characteristic anticodon sequences of major tRNA species from an extreme thermophile,Thermus thermophilusHB8. FEBS Lett 2001. [DOI: 10.1016/0014-5793(86)80667-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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34
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Bajji AC, Davis DR. Synthesis and biophysical characterization of tRNA(Lys,3) anticodon stem-loop RNAs containing the mcm(5)s(2)U nucleoside. Org Lett 2000; 2:3865-8. [PMID: 11101439 DOI: 10.1021/ol006605h] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
[reaction: see text] Phosphoramidite reagents of the naturally occurring modified nucleosides mcm(5)s(2)U and mcm(5)U were synthesized and along with pseudouridine were incorporated into 17-nucleotide lysine tRNA anticodon stem-loop domains. Standard RNA phosphoramidite coupling chemistry allowed us to systematically investigate the thermodynamic effects of nucleoside modification and to correlate thermodynamic trends with qualitative structure effects seen by NMR spectroscopy.
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Affiliation(s)
- A C Bajji
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
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35
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Kumar RK, Davis DR. Synthesis and studies on the effect of 2-thiouridine and 4-thiouridine on sugar conformation and RNA duplex stability. Nucleic Acids Res 1997; 25:1272-80. [PMID: 9092639 PMCID: PMC146581 DOI: 10.1093/nar/25.6.1272] [Citation(s) in RCA: 116] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
In order to understand the effect of 2-thiouridine (s2U) substitution on RNA structure and the potential for stabilization of tRNA codon-anticodon interactions through s2U-34 modification, a pentamer RNA sequence, Gs2UUUC, was synthesized and characterized by NMR spectroscopy. The single strand contains the UUU anticodon sequence of tRNALys with flanking GCs to increase duplex stability. Regiochemical effects of uridine thiolation were determined by comparing the structure and stability of the 2-thiouridine containing oligonucleotide with an identical sequence containing 4-thiouridine (s4U) and also the normal uridine nucleoside. Circular dichroism spectrum indicated an A-form helical conformation for Gs2UUUC which was further confirmed by 2D ROESY NMR experiments. The duplex stability of the three pentamers complexed with a 2'-O-methyl-ribonucleotide complementary strand, GmAmAmAmCm, was determined by UV thermal melting studies and by 1H NMR spectroscopy. The duplex containing s2U has a T m of 30.7 degrees C compared to 19. 0 degrees C for the unmodified control and 14.5 degrees C for the s4U containing duplex. The results from UV experiments were corroborated by imino proton NMR studies that show proton exchange rates, chemical shift differences, and NH proton linewidths indicative of the stability order s2U >U >s4U. The magnitude of the effect of s2U in our model system is comparable to the 20 degrees C stabilization observed by Grosjean and co-workers for 2-thiolation in a codon-anticodon model system composed of two tRNAs with complementary anticodon sequences [Houssier, C., Degee, P., Nicoghosian, K. and Grosjean, H. (1988) J. Biomol. Struct. Dyn., 5, 1259-1266].
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Affiliation(s)
- R K Kumar
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
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36
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Dalluge JJ, Hamamoto T, Horikoshi K, Morita RY, Stetter KO, McCloskey JA. Posttranscriptional modification of tRNA in psychrophilic bacteria. J Bacteriol 1997; 179:1918-23. [PMID: 9068636 PMCID: PMC178914 DOI: 10.1128/jb.179.6.1918-1923.1997] [Citation(s) in RCA: 100] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Posttranscriptional modification in tRNA is known to play a multiplicity of functional roles, including maintenance of tertiary structure and cellular adaptation to environmental factors such as temperature. Nucleoside modification has been studied in unfractionated tRNA from three psychrophilic bacteria (ANT-300 and Vibrio sp. strains 5710 and 29-6) and one psychrotrophic bacterium (Lactobacillus bavaricus). Based on analysis of total enzymatic hydrolysates by liquid chromatography-mass spectrometry, unprecedented low amounts of modification were found in the psychrophiles, particularly from the standpoint of structural diversity of modifications observed. Thirteen to 15 different forms of posttranscriptional modification were found in the psychrophiles, and 10 were found in L. bavaricus, compared with approximately 29 known to occur in bacterial mesophiles and 24 to 31 known to occur in the archaeal hyperthermophiles. The four most abundant modified nucleosides in tRNA from each organism were dihydrouridine, pseudouridine, 7-methylguanosine, and 5-methyluridine. The molar abundances of the latter three nucleosides were comparable to those found in tRNA from Escherichia coli. By contrast, the high levels of dihydrouridine observed in all three psychrophiles are unprecedented for any organism in any of the three phylogenetic domains. tRNA from these organisms contains 40 to 70% more dihydrouridine, on average, than that of the mesophile E. coli or the psychrotroph L. bavaricus. This finding supports the concept that a functional role for dihydrouridine is in maintenance of conformational flexibility of RNA, especially important to organisms growing under conditions where the dynamics of thermal motion are severely compromised. This is in contrast to the role of modifications contained in RNA from thermophiles, which is to reduce regional RNA flexibility and provide structural stability to RNA for adaptation to high temperature.
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Affiliation(s)
- J J Dalluge
- Department of Biochemistry, University of Utah, Salt Lake City 84132, USA
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37
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Sakamoto K, Kawai G, Watanabe S, Niimi T, Hayashi N, Muto Y, Watanabe K, Satoh T, Sekine M, Yokoyama S. NMR studies of the effects of the 5'-phosphate group on conformational properties of 5-methylaminomethyluridine found in the first position of the anticodon of Escherichia coli tRNA(Arg)4. Biochemistry 1996; 35:6533-8. [PMID: 8639601 DOI: 10.1021/bi9526490] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
5-Methylaminomethyluridine (mnm5U) exists in the first position of the anticodon (position 34) of Escherichia coli tRNA4Arg for codons AGA/AGG. In the present study, the temperature dependence of the ribose-puckering equilibrium of pmnm5U was analyzed by proton NMR spectroscopy. Thus, the enthalpy difference (delta H) between the C2'-endo and C3'-endo forms was obtained at 0.65 kcal.mol-1. By comparison of the delta H values of pU and pmnm5U, the 5-substitution was found to increase the relative stability of the C3'-endo form over the C2'-endo form significantly (by 0.56 kcal.mol-1). Furthermore, this conformational "rigidity" was concluded to depend on the 5'-phosphate group, because nucleoside U exhibits only a negligible change in the ribose-puckering equilibrium upon the 5-methylaminomethyl substitution. Further NMR analyses and molecular dynamics calculations revealed that interactions between the 5-methylaminomethyl and 5'-phosphate groups of pmnm5U restrict the conformation about the glycosidic bond to a low anti form, enhancing steric repulsion between the 2-carbonyl and 2'-hydroxyl groups in the C2'-endo form. This intrinsic conformational rigidity of the mnm5U residue in position 34 may contribute to the correct codon recognition.
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Affiliation(s)
- K Sakamoto
- Department of Biophysics and Biochemistry, School of Science, University of Tokyo, Japan
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Palmer JR, Baltrus T, Reeve JN, Daniels CJ. Transfer RNA genes from the hyperthermophilic Archaeon, Methanopyrus kandleri. BIOCHIMICA ET BIOPHYSICA ACTA 1992; 1132:315-8. [PMID: 1384711 DOI: 10.1016/0167-4781(92)90168-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Genes encoding the Leu (GAG), Ser (UGA), Gln (UUG) and Lys (UUU) tRNAs have been cloned and sequenced from the deep sea hyperthermophilic Archaeon, Methanopyrus kandleri. Sequences conforming to the TATA box element established for methanogen promoters are located upstream of the tRNA(Gln) and tRNA(Lys) genes. All four of the tRNA genes appear to encode the 3' terminal CCA residues of the mature tRNA. These methanogen tRNAs are predicted to contain most, but not all, invariant residues and are characterized by a high level of G + C base pairing, consistent with the 98 degrees C optimum growth temperature of M. kandleri.
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Affiliation(s)
- J R Palmer
- Department of Microbiology, Ohio State University, Columbus 43210
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Kawai G, Yamamoto Y, Kamimura T, Masegi T, Sekine M, Hata T, Iimori T, Watanabe T, Miyazawa T, Yokoyama S. Conformational rigidity of specific pyrimidine residues in tRNA arises from posttranscriptional modifications that enhance steric interaction between the base and the 2'-hydroxyl group. Biochemistry 1992; 31:1040-6. [PMID: 1310418 DOI: 10.1021/bi00119a012] [Citation(s) in RCA: 164] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
In order to elucidate roles of the 2'-O-methylation of pyrimidine nucleotide residues of tRNAs, conformations of 2'-O-methyluridylyl(3'----5')uridine (UmpU), 2'-O-methyluridine 3'-monophosphate (Ump), and 2'-O-methyluridine (Um) in 2H2O solution were analyzed by one- and two-dimensional proton NMR spectroscopy and compared with those of related nucleotides and nucleoside. As for UpU and UmpU, the 2'-O-methylation was found to stabilize the C3'-endo form of the 3'-nucleotidyl unit (Up-/Ump-moiety). This stabilization of the C3'-endo form is primarily due to an intraresidue effect, since the conformation of the 5'-nucleotidyl unit (-pU moiety) was only slightly affected by the 2'-O-methylation of the 3'-nucleotide unit. In fact even for Up and Ump, the 2'-O-methylation significantly stabilizes the C3'-endo form by 0.8 kcal/.mol-1. By contrast, for nucleosides (U and Um), the C3'-endo form is slightly stabilized by 0.1 kcal/.mol-1. Accordingly, the stabilization of the C3'-endo form by the 2'-O-methylation is primarily due to the steric repulsion among the 2-carbonyl group, the 2'-O-methyl group and the 3'-phosphate group in the C2'-endo form. For some tRNA species, 2-thiolation of pyrimidine residues is found in positions where the 2'-O-methylation is found for other tRNA species.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- G Kawai
- Department of Biophysics and Biochemistry, Faculty of Science, University of Tokyo, Japan
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40
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Kawai G, Hashizume T, Yasuda M, Miyazawa T, McCloskey JA, Yokoyama S. Conformational Rigidity of N4-Acetyl-2′-O-methylcytidine Found in tRNA of Extremely Thermophilic Archaebacteria (Archaea). ACTA ACUST UNITED AC 1992. [DOI: 10.1080/07328319208021740] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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41
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Ishikawa T, Yoneda F, Tanaka K, Fuji K. Synthesis and properties of oligothymidylate containing sulfur-modified thymidine: effect of thiation of pyrimidine ring on the thermostability and conformation of the duplex. Bioorg Med Chem Lett 1991. [DOI: 10.1016/s0960-894x(01)80458-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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42
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Yokoyama S, Muramatsu T, Kawai G, Miyazawa T. NMR Analyses of Structures and Functions of Modified Nucleosides in Transfer Ribonucleic Acids. ACTA ACUST UNITED AC 1990. [DOI: 10.1080/07328319008045141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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43
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Chapter 9 Modified Uridines in the First Positions of Anti-Codons of TRNAS and Mechanisms of Codon Recognition. ACTA ACUST UNITED AC 1990. [DOI: 10.1016/s0301-4770(08)61495-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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44
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Miyazawa T, Yokoyama S. Structures and functions of proteins and nucleic acids in protein biosynthesis. INT REV PHYS CHEM 1989. [DOI: 10.1080/01442358909353226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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45
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Houssier C, Degée P, Nicoghosian K, Grosjean H. Effect of uridine dethiolation in the anticodon triplet of tRNA(Glu) on its association with tRNA(Phe). J Biomol Struct Dyn 1988; 5:1259-66. [PMID: 2482764 DOI: 10.1080/07391102.1988.10506468] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The effect of U(34) dethiolation on the anticodon-anticodon association between E. coli tRNA(Glu) and yeast tRNA(Phe) has been studied by the temperature jump relaxation technique. An important destabilization upon replacement of the thioketo group of s2U(34) by a keto group, was revealed by a lowering of melting temperature of about 20 degrees C. The measured kinetic parameters indicated that this destabilization effect was originated in an increase of dissociation and a decrease of association rate constants by a factor of 4 to 5. Modifications in both stacking interactions and flexibility in the anticodon loop would be responsible for this effect.
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Affiliation(s)
- C Houssier
- Laboratoire de Chimie Macromoléculaire et Chimie Physique, Université de Liège, Belgium
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46
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Horie N, Hara-Yokoyama M, Yokoyama S, Watanabe K, Kuchino Y, Nishimura S, Miyazawa T. Two tRNAIle1 species from an extreme thermophile, Thermus thermophilus HB8: effect of 2-thiolation of ribothymidine on the thermostability of tRNA. Biochemistry 1985; 24:5711-5. [PMID: 3853464 DOI: 10.1021/bi00342a004] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
From Thermus thermophilus HB8 grown at 65 degrees C, two major tRNAIle species have been purified by column chromatography and polyacrylamide gel electrophoresis. The nucleotide sequence of one of these two tRNAIle1 species (tRNAIle1a) has been determined to be pGGGCGAUUAGCUCAGCUGmGUDAGAGCGCACGCCUGAUt6AAGCGUGAGm7GUCGGUGGs2T psi CAm1AGUCCACCAUCGCCCACCAOH. The nucleotide sequence of the other species (tRNAIle1b) is found to be the same as that of tRNAIle1a except for the modification in position 54; tRNAIle1a has s2T(54) while tRNAIle1b has T(54). The melting temperature of tRNAIle1a is as high as 86.2 degrees C while that of tRNAIle1b is 83.3 degrees C. The single replacement of an oxygen atom (2-carbonyl oxygen) of T(54) by a sulfur atom significantly contributes to the thermostability of the tRNAIle1a species. In addition, the methylation of G(18) and A(58) possibly contributes to the thermostability of T. thermophilus tRNAIle1a and tRNAIle1b species.
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Yokoyama S, Watanabe T, Murao K, Ishikura H, Yamaizumi Z, Nishimura S, Miyazawa T. Molecular mechanism of codon recognition by tRNA species with modified uridine in the first position of the anticodon. Proc Natl Acad Sci U S A 1985; 82:4905-9. [PMID: 3860833 PMCID: PMC390466 DOI: 10.1073/pnas.82.15.4905] [Citation(s) in RCA: 221] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Proton NMR analyses have been made to elucidate the conformational characteristics of modified nucleotides as found in the first position of the anticodon of tRNA [derivatives of 5-methyl-2-thiouridine 5'-monophosphate (pxm5s2U) and derivatives of 5-hydroxyuridine 5'-monophosphate (pxo5U)]. In pxm5s2U, the C3'-endo form is extraordinarily more stable than the C2'-endo form for the ribose ring, because of the combined effects of the 2-thiocarbonyl group and the 5-substituent. By contrast, in pxo5U, the C2'-endo form is much more stable than the C3'-endo form, because of the interaction between the 5-substituent and the 5'-phosphate group. The enthalpy differences between the C2'-endo form and the C3'-endo form have been obtained as 1.1, -0.7, and 0.1 kcal/mol (1 cal = 4.184 J) for pxm5s2U, pxo5U, and unmodified uridine 5'-monophosphate, respectively. These findings lead to the conclusion that xm5s2U in the first position of the anticodon exclusively takes the C3'-endo form to recognize adenosine (but not uridine) as the third letter of the codon, whereas xo5U takes the C2'-endo form as well as the C3'-endo form to recognize adenosine, guanosine, and uridine as the third letter of the codon on ribosome. Accordingly, the biological significance of such modifications of uridine to xm5s2U/xo5U is in the regulation of the conformational rigidity/flexibility in the first position of the anticodon so as to guarantee the correct and efficient translation of codons in protein biosynthesis.
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Yokoyama S, Miyazawa T. Molecular conformations and codon recognition of transfer ribonucleic acids as analyzed by nuclear magnetic resonance. J Mol Struct 1985. [DOI: 10.1016/0022-2860(85)80142-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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