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Bessler L, Sirleaf J, Kampf CJ, Frankowska K, Leszczyńska G, Opatz T, Helm M. Esterification of Cyclic N 6-Threonylcarbamoyladenosine During RNA Sample Preparation. ChemMedChem 2024; 19:e202400115. [PMID: 38630955 DOI: 10.1002/cmdc.202400115] [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: 02/08/2024] [Revised: 04/15/2024] [Accepted: 04/15/2024] [Indexed: 04/19/2024]
Abstract
The continuous deciphering of crucial biological roles of RNA modifications and their involvement in various pathological conditions, together with their key roles in the use of RNA-based therapeutics, has reignited interest in studying the occurrence and identity of non-canonical ribonucleoside structures during the past years. Discovery and structural elucidation of new modified structures is usually achieved by combination of liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) at the nucleoside level and stable isotope labeling experiments. This approach, however, has its pitfalls as demonstrated in the course of the present study: we structurally elucidated a new nucleoside structure that showed significant similarities to the family of (c)t6A modifications and was initially considered a genuine modification, but subsequently turned out to be an in vitro formed glycerol ester of t6A. This artifact is generated from ct6A during RNA hydrolysis upon addition of enzymes stored in glycerol containing buffers in a mildly alkaline milieu, and was moreover shown to undergo an intramolecular transesterification reaction. Our results demand for extra caution, not only in the discovery of new RNA modifications, but also with regard to the quantification of known modified structures, in particular chemically labile modifications, such as ct6A, that might suffer from exposure to putatively harmless reagents during the diverse steps of sample preparation.
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Affiliation(s)
- Larissa Bessler
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| | - Jason Sirleaf
- Department of Chemistry, Johannes Gutenberg University Mainz, Duesbergweg 10-14, 55128, Mainz, Germany
| | - Christopher J Kampf
- Department of Chemistry, Johannes Gutenberg University Mainz, Duesbergweg 10-14, 55128, Mainz, Germany
| | - Katarzyna Frankowska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Łódź, Poland
| | - Grażyna Leszczyńska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Łódź, Poland
| | - Till Opatz
- Department of Chemistry, Johannes Gutenberg University Mainz, Duesbergweg 10-14, 55128, Mainz, Germany
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudingerweg 5, 55128, Mainz, Germany
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2
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Akiyama N, Ishiguro K, Yokoyama T, Miyauchi K, Nagao A, Shirouzu M, Suzuki T. Structural insights into the decoding capability of isoleucine tRNAs with lysidine and agmatidine. Nat Struct Mol Biol 2024; 31:817-825. [PMID: 38538915 DOI: 10.1038/s41594-024-01238-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 01/31/2024] [Indexed: 05/21/2024]
Abstract
The anticodon modifications of transfer RNAs (tRNAs) finetune the codon recognition on the ribosome for accurate translation. Bacteria and archaea utilize the modified cytidines, lysidine (L) and agmatidine (agm2C), respectively, in the anticodon of tRNAIle to decipher AUA codon. L and agm2C contain long side chains with polar termini, but their functions remain elusive. Here we report the cryogenic electron microscopy structures of tRNAsIle recognizing the AUA codon on the ribosome. Both modifications interact with the third adenine of the codon via a unique C-A geometry. The side chains extend toward 3' direction of the mRNA, and the polar termini form hydrogen bonds with 2'-OH of the residue 3'-adjacent to the AUA codon. Biochemical analyses demonstrated that AUA decoding is facilitated by the additional interaction between the polar termini of the modified cytidines and 2'-OH of the fourth mRNA residue. We also visualized cyclic N6-threonylcarbamoyladenosine (ct6A), another tRNA modification, and revealed a molecular basis how ct6A contributes to efficient decoding.
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MESH Headings
- RNA, Transfer, Ile/chemistry
- RNA, Transfer, Ile/metabolism
- RNA, Transfer, Ile/genetics
- Cryoelectron Microscopy
- Anticodon/chemistry
- Anticodon/metabolism
- Ribosomes/metabolism
- Ribosomes/chemistry
- Nucleic Acid Conformation
- Models, Molecular
- Codon/genetics
- Lysine/metabolism
- Lysine/chemistry
- Lysine/analogs & derivatives
- Cytidine/analogs & derivatives
- Cytidine/chemistry
- Cytidine/metabolism
- RNA, Transfer/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- Protein Biosynthesis
- Pyrimidine Nucleosides
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Affiliation(s)
- Naho Akiyama
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Kensuke Ishiguro
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | - Takeshi Yokoyama
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Kenjyo Miyauchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Asuteka Nagao
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Mikako Shirouzu
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan.
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3
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Jin M, Zhang Z, Yu Z, Chen W, Wang X, Lei D, Zhang W. Structure-function analysis of an ancient TsaD-TsaC-SUA5-TcdA modular enzyme reveals a prototype of tRNA t6A and ct6A synthetases. Nucleic Acids Res 2023; 51:8711-8729. [PMID: 37427786 PMCID: PMC10484737 DOI: 10.1093/nar/gkad587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 06/22/2023] [Accepted: 06/29/2023] [Indexed: 07/11/2023] Open
Abstract
N 6-threonylcarbamoyladenosine (t6A) is a post-transcriptional modification found uniquely at position 37 of tRNAs that decipher ANN-codons in the three domains of life. tRNA t6A plays a pivotal role in promoting translational fidelity and maintaining protein homeostasis. The biosynthesis of tRNA t6A requires members from two evolutionarily conserved protein families TsaC/Sua5 and TsaD/Kae1/Qri7, and a varying number of auxiliary proteins. Furthermore, tRNA t6A is modified into a cyclic hydantoin form of t6A (ct6A) by TcdA in bacteria. In this work, we have identified a TsaD-TsaC-SUA5-TcdA modular protein (TsaN) from Pandoraviruses and determined a 3.2 Å resolution cryo-EM structure of P. salinus TsaN. The four domains of TsaN share strong structural similarities with TsaD/Kae1/Qri7 proteins, TsaC/Sua5 proteins, and Escherichia coli TcdA. TsaN catalyzes the formation of threonylcarbamoyladenylate (TC-AMP) using L-threonine, HCO3- and ATP, but does not participate further in tRNA t6A biosynthesis. We report for the first time that TsaN catalyzes a tRNA-independent threonylcarbamoyl modification of adenosine phosphates, leading to t6ADP and t6ATP. Moreover, TsaN is also active in catalyzing tRNA-independent conversion of t6A nucleoside to ct6A. Our results imply that TsaN from Pandoraviruses might be a prototype of the tRNA t6A- and ct6A-modifying enzymes in some cellular organisms.
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Affiliation(s)
- Mengqi Jin
- School of Life Sciences, Key Laboratory of Cell Activities and Stress Adaptation of the Ministry of Education, Lanzhou University, Lanzhou 730000, China
| | - Zelin Zhang
- Key Laboratory for Magnetism and Magnetic Materials of the Ministry of Education, Electron Microscopy Centre of Lanzhou University, Lanzhou University, Lanzhou 730000, China
| | - Zhijiang Yu
- School of Life Sciences, Key Laboratory of Cell Activities and Stress Adaptation of the Ministry of Education, Lanzhou University, Lanzhou 730000, China
| | - Wei Chen
- School of Life Sciences, Key Laboratory of Cell Activities and Stress Adaptation of the Ministry of Education, Lanzhou University, Lanzhou 730000, China
| | - Xiaolei Wang
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Dongsheng Lei
- Key Laboratory for Magnetism and Magnetic Materials of the Ministry of Education, Electron Microscopy Centre of Lanzhou University, Lanzhou University, Lanzhou 730000, China
| | - Wenhua Zhang
- School of Life Sciences, Key Laboratory of Cell Activities and Stress Adaptation of the Ministry of Education, Lanzhou University, Lanzhou 730000, China
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4
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Dodson TA, Nieuwoudt S, Morse CN, Pierre V, Liu C, Senyo SE, Prestwich EG. Ribonucleosides from tRNA in hyperglycemic mammalian cells and diabetic murine cardiac models. Life Sci 2023; 318:121462. [PMID: 36736767 PMCID: PMC9992345 DOI: 10.1016/j.lfs.2023.121462] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 01/24/2023] [Accepted: 01/26/2023] [Indexed: 02/04/2023]
Abstract
AIMS Cardiomyopathy is a diabetic comorbidity with few molecular targets. To address this, we evaluated transfer RNA (tRNA) modifications in the diabetic heart because tRNA modifications have been implicated in diabetic etiologies. MAIN METHODS tRNA was isolated from aorta, apex, and atrial tissue of healthy and diabetic murine hearts and related hyperglycemic cell models. tRNA modifications and canonical ribonucleosides were quantified by liquid-chromatography tandem mass spectrometry (LC-MS/MS) using stable isotope dilution. Correlations between ribonucleosides and diabetic comorbidity pathology were assessed using statistical analyses. KEY FINDINGS Total tRNA ribonucleoside levels were analyzed from cell types and healthy and diabetic murine heart tissue. Each heart structure had characteristic ribonucleoside profiles and quantities. Several ribonucleosides were observed as significantly different in hyperglycemic cells and diabetic tissues. In hyperglycemic models, ribonucleosides N4-acetylcytidine (ac4C), 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U), 5-methylcytidine (m5C), and N1-methylguanosine (m1G) were anomalous. Specific tRNA modifications known to be on murine tRNAIni(CAU) were higher in diabetic heart tissue which suggests that tRNA modifications could be regulating translation in diabetes. SIGNIFICANCE We identified tRNA ribonucleosides and tRNA species associated with hyperglycemia and diabetic etiology.
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Affiliation(s)
- Taylor A Dodson
- Department of Medicinal and Biological Chemistry, College of Pharmacy and Pharmaceutical Sciences, University of Toledo, Toledo, OH, United States
| | - Stephan Nieuwoudt
- Department of Biomedical Engineering, School of Engineering, Case Western Reserve University, Cleveland, OH, United States
| | - Chase N Morse
- Department of Medicinal and Biological Chemistry, College of Pharmacy and Pharmaceutical Sciences, University of Toledo, Toledo, OH, United States
| | - Valinteshley Pierre
- Department of Biomedical Engineering, School of Engineering, Case Western Reserve University, Cleveland, OH, United States
| | - Chao Liu
- Department of Biomedical Engineering, School of Engineering, Case Western Reserve University, Cleveland, OH, United States
| | - Samuel E Senyo
- Department of Biomedical Engineering, School of Engineering, Case Western Reserve University, Cleveland, OH, United States
| | - Erin G Prestwich
- Department of Medicinal and Biological Chemistry, College of Pharmacy and Pharmaceutical Sciences, University of Toledo, Toledo, OH, United States.
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5
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Bo W, Chen Y. Lenvatinib resistance mechanism and potential ways to conquer. Front Pharmacol 2023; 14:1153991. [PMID: 37153782 PMCID: PMC10157404 DOI: 10.3389/fphar.2023.1153991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 04/03/2023] [Indexed: 05/10/2023] Open
Abstract
Lenvatinib (LVN) has been appoved to treat advanced renal cell carcinoma, differentiated thyroid carcinoma, hepatocellular carcinoma. Further other cancer types also have been tried in pre-clinic and clinic without approvation by FDA. The extensive use of lenvastinib in clinical practice is sufficient to illustrate its important therapeutic role. Although the drug resistance has not arised largely in clinical, the studies focusing on the resistance of LVN increasingly. In order to keep up with the latest progress of resistance caused by LVN, we summerized the latest studies from identify published reports. In this review, we found the latest report about resistance caused by lenvatinib, which were contained the hotspot mechanism such as the epithelial-mesenchymal transition, ferroptosis, RNA modification and so on. The potential ways to conquer the resistance of LVN were embraced by nanotechnology, CRISPR technology and traditional combined strategy. The latest literature review of LVN caused resistance would bring some ways for further study of LVN. We call for more attention to the pharmacological parameters of LVN in clinic, which was rarely and would supply key elements for drug itself in human beings and help to find the resistance target or idea for further study.
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Affiliation(s)
- Wentao Bo
- Department of Hepatopancreatobiliary Surgery, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital and Institute, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Yan Chen
- Department of Pharmacy, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital and Institute, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
- *Correspondence: Yan Chen,
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6
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Conservation and Diversification of tRNA t6A-Modifying Enzymes across the Three Domains of Life. Int J Mol Sci 2022; 23:ijms232113600. [PMID: 36362385 PMCID: PMC9654439 DOI: 10.3390/ijms232113600] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 10/28/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022] Open
Abstract
The universal N6-threonylcarbamoyladenosine (t6A) modification occurs at position 37 of tRNAs that decipher codons starting with adenosine. Mechanistically, t6A stabilizes structural configurations of the anticodon stem loop, promotes anticodon–codon pairing and safeguards the translational fidelity. The biosynthesis of tRNA t6A is co-catalyzed by two universally conserved protein families of TsaC/Sua5 (COG0009) and TsaD/Kae1/Qri7 (COG0533). Enzymatically, TsaC/Sua5 protein utilizes the substrates of L-threonine, HCO3−/CO2 and ATP to synthesize an intermediate L-threonylcarbamoyladenylate, of which the threonylcarbamoyl-moiety is subsequently transferred onto the A37 of substrate tRNAs by the TsaD–TsaB –TsaE complex in bacteria or by the KEOPS complex in archaea and eukaryotic cytoplasm, whereas Qri7/OSGEPL1 protein functions on its own in mitochondria. Depletion of tRNA t6A interferes with protein homeostasis and gravely affects the life of unicellular organisms and the fitness of higher eukaryotes. Pathogenic mutations of YRDC, OSGEPL1 and KEOPS are implicated in a number of human mitochondrial and neurological diseases, including autosomal recessive Galloway–Mowat syndrome. The molecular mechanisms underscoring both the biosynthesis and cellular roles of tRNA t6A are presently not well elucidated. This review summarizes current mechanistic understandings of the catalysis, regulation and disease implications of tRNA t6A-biosynthetic machineries of three kingdoms of life, with a special focus on delineating the structure–function relationship from perspectives of conservation and diversity.
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7
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Jora M, Corcoran D, Parungao GG, Lobue PA, Oliveira LFL, Stan G, Addepalli B, Limbach PA. Higher-Energy Collisional Dissociation Mass Spectral Networks for the Rapid, Semi-automated Characterization of Known and Unknown Ribonucleoside Modifications. Anal Chem 2022; 94:13958-13967. [PMID: 36174068 DOI: 10.1021/acs.analchem.2c03172] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Higher-energy collisional dissociation (HCD) of modified ribonucleosides generates characteristic and highly reproducible nucleoside-specific tandem mass spectra (MS/MS). Here, we demonstrate the capability of HCD spectra in combination with spectral matching for the semi-automated characterization of ribonucleosides. This process involved the generation of an HCD spectral library and the establishment of a mass spectral network for rapid detection with high sensitivity and specificity in a retention time-independent fashion. Systematic spectral matching analysis of the MS/MS spectra of tRNA hydrolysates from different organisms has helped us to uncover evidence for the existence of novel ribonucleoside modifications such as s2Cm and OHyW-14. Such an untargeted label-free approach has the potential to be integrated with other methods, including those that use isotope labeling, to simplify the characterization of unknown modified ribonucleosides. These findings suggest the compilation of a universal spectral network, for the characterization of known and unknown ribonucleosides, could accelerate discoveries in the epitranscriptome.
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Affiliation(s)
- Manasses Jora
- Department of Chemistry, University of Cincinnati, P.O. Box 210172, Cincinnati, Ohio 45221-0172, United States
| | - Daniel Corcoran
- Department of Chemistry, University of Cincinnati, P.O. Box 210172, Cincinnati, Ohio 45221-0172, United States
| | - Gwenn G Parungao
- Department of Chemistry, University of Cincinnati, P.O. Box 210172, Cincinnati, Ohio 45221-0172, United States
| | - Peter A Lobue
- Department of Chemistry, University of Cincinnati, P.O. Box 210172, Cincinnati, Ohio 45221-0172, United States
| | - Luiz F L Oliveira
- Department of Chemistry, University of Cincinnati, P.O. Box 210172, Cincinnati, Ohio 45221-0172, United States
| | - George Stan
- Department of Chemistry, University of Cincinnati, P.O. Box 210172, Cincinnati, Ohio 45221-0172, United States
| | - Balasubrahmanyam Addepalli
- Department of Chemistry, University of Cincinnati, P.O. Box 210172, Cincinnati, Ohio 45221-0172, United States
| | - Patrick A Limbach
- Department of Chemistry, University of Cincinnati, P.O. Box 210172, Cincinnati, Ohio 45221-0172, United States
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8
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Dound AS, Fandilolu PM, Sonawane KD. Structural Significance of Conformational Preferences and Ribose-Ring-Puckering of Hyper Modified Nucleotide 5'-Monophosphate 2-Methylthio Cyclic N 6-Threonylcarbamoyladenosine (p-ms 2ct 6A) Present at 37th Position in Anticodon Loop of tRNA Lys. Cell Biochem Biophys 2022; 80:665-680. [PMID: 35965304 DOI: 10.1007/s12013-022-01086-0] [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: 07/06/2021] [Accepted: 07/28/2022] [Indexed: 12/01/2022]
Abstract
Structural significance of conformational preferences and ribose ring puckering of newly discovered hyper modified nucleotide, 5'-monophosphate 2-methylthio cyclic N6-threonylcarbamoyladenosine (p-ms2ct6A) have been investigated using quantum chemical semi-empirical RM1 and molecular dynamics simulation techniques. Automated geometry optimization of most stable structure of p-ms2ct6A has also been carried out with the help of abinitio (HF SCF, DFT) as well as semi empirical quantum chemical (RM1, AM1, PM3, and PM6) methods. Most stable structure of p-ms2ct6A is stabilized by intramolecular interactions between N(3)…HC(2'), N(1)…HC(16), O(13)…HC(15), and O(13)…HO(14). The torsion angles alpha (α) and beta (β) show the significant characteristic patterns with the involvement of intramolecular hydrogen bonding to provide stability to the p-ms2ct6A. Further, molecular dynamics simulations of p-ms2ct6A revealed the role of ribose sugar ring puckering i.e. C2'-endo and C3'-endo on the structural dynamics of ms2ct6A side chain. The modified nucleotide p-ms2ct6A periodically prefers both the C2'-endo and C3'-endo sugar with 'anti' and 'syn' conformations. This property of p-ms2ct6A could be useful to recognize the starting ANN codons. All atom explicit MD simulation of anticodon loop (ACL) of tRNALys of Bacillus subtilis containing ms2ct6A at 37th position showed the U-turn feature, base stacking ability with other adjacent bases and hydrogen bonding interactions similar to the isolated base p-ms2ct6A. The ribose sugar puckering contributes to the orientation of the side chain conformation of p-ms2ct6A. Thus, the present study could be helpful to understand the structure-function relationship of the hypermodified nucleoside, ms2ct6A in recognition of the proper codons AAA/AAG during protein biosynthesis.
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Affiliation(s)
- Ambika S Dound
- Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Kolhapur, 416 004, Maharashtra, India
| | - Prayagraj M Fandilolu
- Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Kolhapur, 416 004, Maharashtra, India
| | - Kailas D Sonawane
- Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Kolhapur, 416 004, Maharashtra, India.
- Department of Microbiology, Shivaji University, Kolhapur, 416004, Maharashtra, India.
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9
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D’Esposito RJ, Myers CA, Chen AA, Vangaveti S. Challenges with Simulating Modified RNA: Insights into Role and Reciprocity of Experimental and Computational Approaches. Genes (Basel) 2022; 13:genes13030540. [PMID: 35328093 PMCID: PMC8949676 DOI: 10.3390/genes13030540] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 01/12/2023] Open
Abstract
RNA is critical to a broad spectrum of biological and viral processes. This functional diversity is a result of their dynamic nature; the variety of three-dimensional structures that they can fold into; and a host of post-transcriptional chemical modifications. While there are many experimental techniques to study the structural dynamics of biomolecules, molecular dynamics simulations (MDS) play a significant role in complementing experimental data and providing mechanistic insights. The accuracy of the results obtained from MDS is determined by the underlying physical models i.e., the force-fields, that steer the simulations. Though RNA force-fields have received a lot of attention in the last decade, they still lag compared to their protein counterparts. The chemical diversity imparted by the RNA modifications adds another layer of complexity to an already challenging problem. Insight into the effect of RNA modifications upon RNA folding and dynamics is lacking due to the insufficiency or absence of relevant experimental data. This review provides an overview of the state of MDS of modified RNA, focusing on the challenges in parameterization of RNA modifications as well as insights into relevant reference experiments necessary for their calibration.
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Affiliation(s)
- Rebecca J. D’Esposito
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA; (R.J.D.); (A.A.C.)
| | - Christopher A. Myers
- Department of Physics, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA;
| | - Alan A. Chen
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA; (R.J.D.); (A.A.C.)
- The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA
| | - Sweta Vangaveti
- The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA
- Correspondence:
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10
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Frankowska K, Sochacka E. New efficient synthesis of tRNA related adenosines bearing the hydantoin ring (ct6A, ms2ct6A) by intramolecular cyclization of N6-(N-Boc-α-aminoacyl)-adenosine derivatives. Chembiochem 2022; 23:e202100655. [PMID: 34997683 DOI: 10.1002/cbic.202100655] [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: 11/29/2021] [Revised: 01/07/2022] [Indexed: 11/10/2022]
Abstract
A novel and efficient way for synthesis of N6-hydantoin modified adenosines, which utilizes readily available N6-(N-Boc-α-aminoacyl)-adenosine derivatives, was developed. The procedure is based on the epimerization free Tf2O-mediated conversion of the Boc group into an isocyanate moiety, followed by intramolecular cyclization. Using this method two recently discovered hydantoin modified tRNA adenosines, i.e. cyclic N6-threonylcarbamoyl-adenosine (ct6A) and 2-methylthio-N6-threonylcarbamoyladenosine (ms2ct6A) were prepared in good yields.
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Affiliation(s)
- Katarzyna Frankowska
- Lodz University of Technology: Politechnika Lodzka, Faculty of Chemistry, POLAND
| | - Elzbieta Sochacka
- Lodz University of Technology, Faculty of Chemistry, ul. Żeromskiego 116, 90-924, Łódź, POLAND
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11
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Beenstock J, Sicheri F. The structural and functional workings of KEOPS. Nucleic Acids Res 2021; 49:10818-10834. [PMID: 34614169 PMCID: PMC8565320 DOI: 10.1093/nar/gkab865] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/09/2021] [Accepted: 10/04/2021] [Indexed: 11/14/2022] Open
Abstract
KEOPS (Kinase, Endopeptidase and Other Proteins of Small size) is a five-subunit protein complex that is highly conserved in eukaryotes and archaea and is essential for the fitness of cells and for animal development. In humans, mutations in KEOPS genes underlie Galloway-Mowat syndrome, which manifests in severe microcephaly and renal dysfunction that lead to childhood death. The Kae1 subunit of KEOPS catalyzes the universal and essential tRNA modification N6-threonylcarbamoyl adenosine (t6A), while the auxiliary subunits Cgi121, the kinase/ATPase Bud32, Pcc1 and Gon7 play a supporting role. Kae1 orthologs are also present in bacteria and mitochondria but function in distinct complexes with proteins that are not related in structure or function to the auxiliary subunits of KEOPS. Over the past 15 years since its discovery, extensive study in the KEOPS field has provided many answers towards understanding the roles that KEOPS plays in cells and in human disease and how KEOPS carries out these functions. In this review, we provide an overview into recent advances in the study of KEOPS and illuminate exciting future directions.
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Affiliation(s)
- Jonah Beenstock
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X5, Canada
| | - Frank Sicheri
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X5, Canada.,Department of Molecular Genetics, University of Toronto, Ontario, M5S 1A8, Canada.,Department of Biochemistry, University of Toronto, Ontario, M5S 1A8, Canada
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12
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Kaiser S, Byrne SR, Ammann G, Asadi Atoi P, Borland K, Brecheisen R, DeMott MS, Gehrke T, Hagelskamp F, Heiss M, Yoluç Y, Liu L, Zhang Q, Dedon PC, Cao B, Kellner S. Strategien zur Vermeidung von Artefakten in der massenspektrometrischen Epitranskriptomanalytik. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202106215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Steffen Kaiser
- Ludwig-Maximilians Universität München Butenandtstr. 5–13 81137 München Deutschland
- Institut für Pharmazeutische Chemie Goethe-Universität Frankfurt Max-von-Laue-Str. 9 60438 Frankfurt Deutschland
| | - Shane R. Byrne
- Department of Biological Engineering and Center for Environmental Health Sciences Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Gregor Ammann
- Ludwig-Maximilians Universität München Butenandtstr. 5–13 81137 München Deutschland
| | - Paria Asadi Atoi
- Ludwig-Maximilians Universität München Butenandtstr. 5–13 81137 München Deutschland
| | - Kayla Borland
- Ludwig-Maximilians Universität München Butenandtstr. 5–13 81137 München Deutschland
| | | | - Michael S. DeMott
- Department of Biological Engineering and Center for Environmental Health Sciences Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Tim Gehrke
- Ella Biotech GmbH 82152 München Deutschland
| | - Felix Hagelskamp
- Ludwig-Maximilians Universität München Butenandtstr. 5–13 81137 München Deutschland
| | - Matthias Heiss
- Ludwig-Maximilians Universität München Butenandtstr. 5–13 81137 München Deutschland
| | - Yasemin Yoluç
- Ludwig-Maximilians Universität München Butenandtstr. 5–13 81137 München Deutschland
| | - Lili Liu
- College of Life Sciences Qufu Normal University Qufu Shandong 273165 China
| | - Qinghua Zhang
- College of Life Sciences Qufu Normal University Qufu Shandong 273165 China
| | - Peter C. Dedon
- Department of Biological Engineering and Center for Environmental Health Sciences Massachusetts Institute of Technology Cambridge MA 02139 USA
- Antimicrobial Resistance Interdisciplinary Research Group Singapore-Massachusetts Institute of Technology Alliance for Research and Technology 138602 Singapore Singapur
| | - Bo Cao
- College of Life Sciences Qufu Normal University Qufu Shandong 273165 China
| | - Stefanie Kellner
- Ludwig-Maximilians Universität München Butenandtstr. 5–13 81137 München Deutschland
- Institut für Pharmazeutische Chemie Goethe-Universität Frankfurt Max-von-Laue-Str. 9 60438 Frankfurt Deutschland
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13
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Kaiser S, Byrne SR, Ammann G, Asadi Atoi P, Borland K, Brecheisen R, DeMott MS, Gehrke T, Hagelskamp F, Heiss M, Yoluç Y, Liu L, Zhang Q, Dedon PC, Cao B, Kellner S. Strategies to Avoid Artifacts in Mass Spectrometry-Based Epitranscriptome Analyses. Angew Chem Int Ed Engl 2021; 60:23885-23893. [PMID: 34339593 PMCID: PMC8597057 DOI: 10.1002/anie.202106215] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Indexed: 11/05/2022]
Abstract
In this report, we perform structure validation of recently reported RNA phosphorothioate (PT) modifications, a new set of epitranscriptome marks found in bacteria and eukaryotes including humans. By comparing synthetic PT-containing diribonucleotides with native species in RNA hydrolysates by high-resolution mass spectrometry (MS), metabolic stable isotope labeling, and PT-specific iodine-desulfurization, we disprove the existence of PTs in RNA from E. coli, S. cerevisiae, human cell lines, and mouse brain. Furthermore, we discuss how an MS artifact led to the initial misidentification of 2'-O-methylated diribonucleotides as RNA phosphorothioates. To aid structure validation of new nucleic acid modifications, we present a detailed guideline for MS analysis of RNA hydrolysates, emphasizing how the chosen RNA hydrolysis protocol can be a decisive factor in discovering and quantifying RNA modifications in biological samples.
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Affiliation(s)
- Steffen Kaiser
- Ludwig-Maximilians Universität MünchenButenandtstr. 5–1381137MünchenDeutschland
- Institute of Pharmaceutical ChemistryGoethe-University FrankfurtMax-von-Laue-Str. 960438FrankfurtGermany
| | - Shane R. Byrne
- Department of Biological Engineering and Center for Environmental Health SciencesMassachusetts Institute of TechnologyCambridgeMA02139USA
| | - Gregor Ammann
- Ludwig-Maximilians Universität MünchenButenandtstr. 5–1381137MünchenDeutschland
| | - Paria Asadi Atoi
- Ludwig-Maximilians Universität MünchenButenandtstr. 5–1381137MünchenDeutschland
| | - Kayla Borland
- Ludwig-Maximilians Universität MünchenButenandtstr. 5–1381137MünchenDeutschland
| | | | - Michael S. DeMott
- Department of Biological Engineering and Center for Environmental Health SciencesMassachusetts Institute of TechnologyCambridgeMA02139USA
| | | | - Felix Hagelskamp
- Ludwig-Maximilians Universität MünchenButenandtstr. 5–1381137MünchenDeutschland
| | - Matthias Heiss
- Ludwig-Maximilians Universität MünchenButenandtstr. 5–1381137MünchenDeutschland
| | - Yasemin Yoluç
- Ludwig-Maximilians Universität MünchenButenandtstr. 5–1381137MünchenDeutschland
| | - Lili Liu
- College of Life SciencesQufu Normal UniversityQufuShandong273165China
| | - Qinghua Zhang
- College of Life SciencesQufu Normal UniversityQufuShandong273165China
| | - Peter C. Dedon
- Department of Biological Engineering and Center for Environmental Health SciencesMassachusetts Institute of TechnologyCambridgeMA02139USA
- Antimicrobial Resistance Interdisciplinary Research GroupSingapore-Massachusetts Institute of Technology Alliance for Research and Technology138602SingaporeSingapore
| | - Bo Cao
- College of Life SciencesQufu Normal UniversityQufuShandong273165China
| | - Stefanie Kellner
- Ludwig-Maximilians Universität MünchenButenandtstr. 5–1381137MünchenDeutschland
- Institute of Pharmaceutical ChemistryGoethe-University FrankfurtMax-von-Laue-Str. 960438FrankfurtGermany
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14
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Kopina BJ, Missoury S, Collinet B, Fulton MG, Cirio C, van Tilbeurgh H, Lauhon CT. Structure of a reaction intermediate mimic in t6A biosynthesis bound in the active site of the TsaBD heterodimer from Escherichia coli. Nucleic Acids Res 2021; 49:2141-2160. [PMID: 33524148 PMCID: PMC7913687 DOI: 10.1093/nar/gkab026] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 12/21/2020] [Accepted: 01/15/2021] [Indexed: 11/14/2022] Open
Abstract
The tRNA modification N6-threonylcarbamoyladenosine (t6A) is universally conserved in all organisms. In bacteria, the biosynthesis of t6A requires four proteins (TsaBCDE) that catalyze the formation of t6A via the unstable intermediate l-threonylcarbamoyl-adenylate (TC-AMP). While the formation and stability of this intermediate has been studied in detail, the mechanism of its transfer to A37 in tRNA is poorly understood. To investigate this step, the structure of the TsaBD heterodimer from Escherichia coli has been solved bound to a stable phosphonate isosteric mimic of TC-AMP. The phosphonate inhibits t6A synthesis in vitro with an IC50 value of 1.3 μM in the presence of millimolar ATP and L-threonine. The inhibitor binds to TsaBD by coordination to the active site Zn atom via an oxygen atom from both the phosphonate and the carboxylate moieties. The bound conformation of the inhibitor suggests that the catalysis exploits a putative oxyanion hole created by a conserved active site loop of TsaD and that the metal essentially serves as a binding scaffold for the intermediate. The phosphonate bound crystal structure should be useful for the rational design of potent, drug-like small molecule inhibitors as mechanistic probes or potentially novel antibiotics.
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Affiliation(s)
- Brett J Kopina
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison, WI 53705, USA
| | - Sophia Missoury
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Bruno Collinet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.,Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Sorbonne-Université, UMR7590 CNRS, MNHN, Paris, France
| | - Mark G Fulton
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison, WI 53705, USA
| | - Charles Cirio
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Herman van Tilbeurgh
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Charles T Lauhon
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison, WI 53705, USA
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15
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The expanding world of tRNA modifications and their disease relevance. Nat Rev Mol Cell Biol 2021; 22:375-392. [PMID: 33658722 DOI: 10.1038/s41580-021-00342-0] [Citation(s) in RCA: 271] [Impact Index Per Article: 90.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/26/2021] [Indexed: 02/08/2023]
Abstract
Transfer RNA (tRNA) is an adapter molecule that links a specific codon in mRNA with its corresponding amino acid during protein synthesis. tRNAs are enzymatically modified post-transcriptionally. A wide variety of tRNA modifications are found in the tRNA anticodon, which are crucial for precise codon recognition and reading frame maintenance, thereby ensuring accurate and efficient protein synthesis. In addition, tRNA-body regions are also frequently modified and thus stabilized in the cell. Over the past two decades, 16 novel tRNA modifications were discovered in various organisms, and the chemical space of tRNA modification continues to expand. Recent studies have revealed that tRNA modifications can be dynamically altered in response to levels of cellular metabolites and environmental stresses. Importantly, we now understand that deficiencies in tRNA modification can have pathological consequences, which are termed 'RNA modopathies'. Dysregulation of tRNA modification is involved in mitochondrial diseases, neurological disorders and cancer.
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16
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Yoluç Y, Ammann G, Barraud P, Jora M, Limbach PA, Motorin Y, Marchand V, Tisné C, Borland K, Kellner S. Instrumental analysis of RNA modifications. Crit Rev Biochem Mol Biol 2021; 56:178-204. [PMID: 33618598 DOI: 10.1080/10409238.2021.1887807] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Organisms from all domains of life invest a substantial amount of energy for the introduction of RNA modifications into nearly all transcripts studied to date. Instrumental analysis of RNA can focus on the modified residues and reveal the function of these epitranscriptomic marks. Here, we will review recent advances and breakthroughs achieved by NMR spectroscopy, sequencing, and mass spectrometry of the epitranscriptome.
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Affiliation(s)
- Yasemin Yoluç
- Department of Chemistry, Ludwig Maximilians University, Munich, Germany
| | - Gregor Ammann
- Department of Chemistry, Ludwig Maximilians University, Munich, Germany
| | - Pierre Barraud
- Expression génétique microbienne, UMR 8261, CNRS, Institut de biologie physico-chimique, IBPC, Université de Paris, Paris, France
| | - Manasses Jora
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
| | - Patrick A Limbach
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
| | - Yuri Motorin
- Université de Lorraine, CNRS, UMR7365 IMoPA, Nancy, France
| | - Virginie Marchand
- Université de Lorraine, CNRS, INSERM, Epitranscriptomics and RNA Sequencing Core facility, UM S2008, IBSLor, Nancy, France
| | - Carine Tisné
- Expression génétique microbienne, UMR 8261, CNRS, Institut de biologie physico-chimique, IBPC, Université de Paris, Paris, France
| | - Kayla Borland
- Department of Chemistry, Ludwig Maximilians University, Munich, Germany
| | - Stefanie Kellner
- Department of Chemistry, Ludwig Maximilians University, Munich, Germany.,Institute of Pharmaceutical Chemistry, Goethe-University, Frankfurt, Germany
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17
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Jora M, Borland K, Abernathy S, Zhao R, Kelley M, Kellner S, Addepalli B, Limbach PA. Chemical Amination/Imination of Carbonothiolated Nucleosides During RNA Hydrolysis. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202010793] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Manasses Jora
- Rieveschl Laboratories for Mass Spectrometry Department of Chemistry University of Cincinnati PO Box 210172 Cincinnati OH 45221-0172 USA
| | - Kayla Borland
- Department of Chemistry Ludwig Maximilians University Munich Butenandtstr. 5–13 81377 Munich Germany
| | - Scott Abernathy
- Rieveschl Laboratories for Mass Spectrometry Department of Chemistry University of Cincinnati PO Box 210172 Cincinnati OH 45221-0172 USA
| | - Ruoxia Zhao
- Rieveschl Laboratories for Mass Spectrometry Department of Chemistry University of Cincinnati PO Box 210172 Cincinnati OH 45221-0172 USA
| | - Melissa Kelley
- Rieveschl Laboratories for Mass Spectrometry Department of Chemistry University of Cincinnati PO Box 210172 Cincinnati OH 45221-0172 USA
| | - Stefanie Kellner
- Department of Chemistry Ludwig Maximilians University Munich Butenandtstr. 5–13 81377 Munich Germany
| | - Balasubrahmanyam Addepalli
- Rieveschl Laboratories for Mass Spectrometry Department of Chemistry University of Cincinnati PO Box 210172 Cincinnati OH 45221-0172 USA
| | - Patrick A. Limbach
- Rieveschl Laboratories for Mass Spectrometry Department of Chemistry University of Cincinnati PO Box 210172 Cincinnati OH 45221-0172 USA
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18
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Seelam Prabhakar P, Takyi NA, Wetmore SD. Posttranscriptional modifications at the 37th position in the anticodon stem-loop of tRNA: structural insights from MD simulations. RNA (NEW YORK, N.Y.) 2021; 27:202-220. [PMID: 33214333 PMCID: PMC7812866 DOI: 10.1261/rna.078097.120] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 11/16/2020] [Indexed: 06/11/2023]
Abstract
Transfer RNA (tRNA) is the most diversely modified RNA. Although the strictly conserved purine position 37 in the anticodon stem-loop undergoes modifications that are phylogenetically distributed, we do not yet fully understand the roles of these modifications. Therefore, molecular dynamics simulations are used to provide molecular-level details for how such modifications impact the structure and function of tRNA. A focus is placed on three hypermodified base families that include the parent i6A, t6A, and yW modifications, as well as derivatives. Our data reveal that the hypermodifications exhibit significant conformational flexibility in tRNA, which can be modulated by additional chemical functionalization. Although the overall structure of the tRNA anticodon stem remains intact regardless of the modification considered, the anticodon loop must rearrange to accommodate the bulky, dynamic hypermodifications, which includes changes in the nucleotide glycosidic and backbone conformations, and enhanced or completely new nucleobase-nucleobase interactions compared to unmodified tRNA or tRNA containing smaller (m1G) modifications at the 37th position. Importantly, the extent of the changes in the anticodon loop is influenced by the addition of small functional groups to parent modifications, implying each substituent can further fine-tune tRNA structure. Although the dominant conformation of the ASL is achieved in different ways for each modification, the molecular features of all modified tRNA drive the ASL domain to adopt the functional open-loop conformation. Importantly, the impact of the hypermodifications is preserved in different sequence contexts. These findings highlight the likely role of regulating mRNA structure and translation.
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MESH Headings
- Adenosine/analogs & derivatives
- Adenosine/metabolism
- Anticodon/chemistry
- Anticodon/genetics
- Anticodon/metabolism
- Base Pairing
- Base Sequence
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Isopentenyladenosine/chemistry
- Isopentenyladenosine/metabolism
- Molecular Dynamics Simulation
- Nucleic Acid Conformation
- Nucleosides/chemistry
- Nucleosides/metabolism
- RNA Processing, Post-Transcriptional
- RNA, Transfer, Lys/chemistry
- RNA, Transfer, Lys/genetics
- RNA, Transfer, Lys/metabolism
- RNA, Transfer, Phe/chemistry
- RNA, Transfer, Phe/genetics
- RNA, Transfer, Phe/metabolism
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Affiliation(s)
- Preethi Seelam Prabhakar
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
| | - Nathania A Takyi
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
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19
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Debiec K, Sochacka E. Efficient access to 3'- O-phosphoramidite derivatives of tRNA related N 6-threonylcarbamoyladenosine (t 6A) and 2-methylthio- N 6-threonylcarbamoyladenosine (ms 2t 6A). RSC Adv 2021; 11:1992-1999. [PMID: 35424152 PMCID: PMC8693639 DOI: 10.1039/d0ra09803e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 12/15/2020] [Indexed: 12/11/2022] Open
Abstract
An efficient method of ureido linkage formation during epimerization-free one-pot synthesis of protected hypermodified N 6-threonylcarbamoyladenosine (t6A) and its 2-SMe analog (ms2t6A) was developed. The method is based on a Tf2O-mediated direct conversion of the N-Boc-protecting group of N-Boc-threonine into the isocyanate derivative, followed by reaction with the N 6 exo-amine function of the sugar protected nucleoside (yield 86-94%). Starting from 2',3',5'-tri-O-acetyl protected adenosine or 2-methylthioadenosine, the corresponding 3'-O-phosphoramidite monomers were obtained in 48% and 42% overall yield (5 step synthesis). In an analogous synthesis, using the 2'-O-(tert-butyldimethylsilyl)-3',5'-O-(di-tert-butylsilylene) protection system at the adenosine ribose moiety, the t6A-phosphoramidite monomer was obtained in a less laborious manner and in a remarkably better yield of 74%.
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Affiliation(s)
- Katarzyna Debiec
- 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
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20
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Jora M, Borland K, Abernathy S, Zhao R, Kelley M, Kellner S, Addepalli B, Limbach PA. Chemical Amination/Imination of Carbonothiolated Nucleosides During RNA Hydrolysis. Angew Chem Int Ed Engl 2020; 60:3961-3966. [DOI: 10.1002/anie.202010793] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 10/17/2020] [Indexed: 01/10/2023]
Affiliation(s)
- Manasses Jora
- Rieveschl Laboratories for Mass Spectrometry Department of Chemistry University of Cincinnati PO Box 210172 Cincinnati OH 45221-0172 USA
| | - Kayla Borland
- Department of Chemistry Ludwig Maximilians University Munich Butenandtstr. 5–13 81377 Munich Germany
| | - Scott Abernathy
- Rieveschl Laboratories for Mass Spectrometry Department of Chemistry University of Cincinnati PO Box 210172 Cincinnati OH 45221-0172 USA
| | - Ruoxia Zhao
- Rieveschl Laboratories for Mass Spectrometry Department of Chemistry University of Cincinnati PO Box 210172 Cincinnati OH 45221-0172 USA
| | - Melissa Kelley
- Rieveschl Laboratories for Mass Spectrometry Department of Chemistry University of Cincinnati PO Box 210172 Cincinnati OH 45221-0172 USA
| | - Stefanie Kellner
- Department of Chemistry Ludwig Maximilians University Munich Butenandtstr. 5–13 81377 Munich Germany
| | - Balasubrahmanyam Addepalli
- Rieveschl Laboratories for Mass Spectrometry Department of Chemistry University of Cincinnati PO Box 210172 Cincinnati OH 45221-0172 USA
| | - Patrick A. Limbach
- Rieveschl Laboratories for Mass Spectrometry Department of Chemistry University of Cincinnati PO Box 210172 Cincinnati OH 45221-0172 USA
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21
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Sun C, Limbach PA, Addepalli B. Characterization of UVA-Induced Alterations to Transfer RNA Sequences. Biomolecules 2020; 10:E1527. [PMID: 33171700 PMCID: PMC7695249 DOI: 10.3390/biom10111527] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 11/02/2020] [Accepted: 11/05/2020] [Indexed: 02/07/2023] Open
Abstract
Ultraviolet radiation (UVR) adversely affects the integrity of DNA, RNA, and their nucleoside modifications. By employing liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based RNA modification mapping approaches, we identified the transfer RNA (tRNA) regions most vulnerable to photooxidation. Photooxidative damage to the anticodon and variable loop regions was consistently observed in both modified and unmodified sequences of tRNA upon UVA (λ 370 nm) exposure. The extent of oxidative damage measured in terms of oxidized guanosine, however, was higher in unmodified RNA compared to its modified version, suggesting an auxiliary role for nucleoside modifications. The type of oxidation product formed in the anticodon stem-loop region varied with the modification type, status, and whether the tRNA was inside or outside the cell during exposure. Oligonucleotide-based characterization of tRNA following UVA exposure also revealed the presence of novel photoproducts and stable intermediates not observed by nucleoside analysis alone. This approach provides sequence-specific information revealing potential hotspots for UVA-induced damage in tRNAs.
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Affiliation(s)
| | | | - Balasubrahmanyam Addepalli
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221-0172, USA; (C.S.); (P.A.L.)
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22
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Swinehart W, Deutsch C, Sarachan KL, Luthra A, Bacusmo JM, de Crécy-Lagard V, Swairjo MA, Agris PF, Iwata-Reuyl D. Specificity in the biosynthesis of the universal tRNA nucleoside N6-threonylcarbamoyl adenosine (t 6A)-TsaD is the gatekeeper. RNA (NEW YORK, N.Y.) 2020; 26:1094-1103. [PMID: 32385138 PMCID: PMC7430679 DOI: 10.1261/rna.075747.120] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 05/03/2020] [Indexed: 06/11/2023]
Abstract
N6-threonylcarbamoyl adenosine (t6A) is a nucleoside modification found in all kingdoms of life at position 37 of tRNAs decoding ANN codons, which functions in part to restrict translation initiation to AUG and suppress frameshifting at tandem ANN codons. In Bacteria the proteins TsaB, TsaC (or C2), TsaD, and TsaE, comprise the biosynthetic apparatus responsible for t6A formation. TsaC(C2) and TsaD harbor the relevant active sites, with TsaC(C2) catalyzing the formation of the intermediate threonylcarbamoyladenosine monophosphate (TC-AMP) from ATP, threonine, and CO2, and TsaD catalyzing the transfer of the threonylcarbamoyl moiety from TC-AMP to A37 of substrate tRNAs. Several related modified nucleosides, including hydroxynorvalylcarbamoyl adenosine (hn6A), have been identified in select organisms, but nothing is known about their biosynthesis. To better understand the mechanism and structural constraints on t6A formation, and to determine if related modified nucleosides are formed via parallel biosynthetic pathways or the t6A pathway, we carried out biochemical and biophysical investigations of the t6A systems from E. coli and T. maritima to address these questions. Using kinetic assays of TsaC(C2), tRNA modification assays, and NMR, our data demonstrate that TsaC(C2) exhibit relaxed substrate specificity, producing a variety of TC-AMP analogs that can differ in both the identity of the amino acid and nucleotide component, whereas TsaD displays more stringent specificity, but efficiently produces hn6A in E. coli and T. maritima tRNA. Thus, in organisms that contain modifications such as hn6A in their tRNA, we conclude that their origin is due to formation via the t6A pathway.
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Affiliation(s)
- William Swinehart
- Department of Chemistry, Portland State University, Portland, Oregon 97201, USA
| | - Christopher Deutsch
- Department of Chemistry, Portland State University, Portland, Oregon 97201, USA
| | - Kathryn L Sarachan
- The RNA Institute, State University of New York, Albany, New York 12222, USA
| | - Amit Luthra
- Department of Chemistry and Biochemistry, and The Viral Information Institute, San Diego State University, San Diego, California 92182, USA
| | - Jo Marie Bacusmo
- Department of Microbiology and Cell Science, University of Florida, Gainsville, Florida 32611, USA
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainsville, Florida 32611, USA
| | - Manal A Swairjo
- Department of Chemistry and Biochemistry, and The Viral Information Institute, San Diego State University, San Diego, California 92182, USA
| | - Paul F Agris
- The RNA Institute, State University of New York, Albany, New York 12222, USA
| | - Dirk Iwata-Reuyl
- Department of Chemistry, Portland State University, Portland, Oregon 97201, USA
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23
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Bartosik K, Debiec K, Czarnecka A, Sochacka E, Leszczynska G. Synthesis of Nucleobase-Modified RNA Oligonucleotides by Post-Synthetic Approach. Molecules 2020; 25:E3344. [PMID: 32717917 PMCID: PMC7436257 DOI: 10.3390/molecules25153344] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 07/15/2020] [Accepted: 07/20/2020] [Indexed: 12/12/2022] Open
Abstract
The chemical synthesis of modified oligoribonucleotides represents a powerful approach to study the structure, stability, and biological activity of RNAs. Selected RNA modifications have been proven to enhance the drug-like properties of RNA oligomers providing the oligonucleotide-based therapeutic agents in the antisense and siRNA technologies. The important sites of RNA modification/functionalization are the nucleobase residues. Standard phosphoramidite RNA chemistry allows the site-specific incorporation of a large number of functional groups to the nucleobase structure if the building blocks are synthetically obtainable and stable under the conditions of oligonucleotide chemistry and work-up. Otherwise, the chemically modified RNAs are produced by post-synthetic oligoribonucleotide functionalization. This review highlights the post-synthetic RNA modification approach as a convenient and valuable method to introduce a wide variety of nucleobase modifications, including recently discovered native hypermodified functional groups, fluorescent dyes, photoreactive groups, disulfide crosslinks, and nitroxide spin labels.
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Affiliation(s)
| | | | | | | | - Grazyna Leszczynska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland; (K.B.); (K.D.); (A.C.); (E.S.)
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24
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Kimura S, Srisuknimit V, Waldor MK. Probing the diversity and regulation of tRNA modifications. Curr Opin Microbiol 2020; 57:41-48. [PMID: 32663792 DOI: 10.1016/j.mib.2020.06.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/28/2020] [Accepted: 06/08/2020] [Indexed: 01/21/2023]
Abstract
Transfer RNAs (tRNAs) are non-coding RNAs essential for protein synthesis. tRNAs are heavily decorated with a variety of post-transcriptional modifications (tRNA modifications). Recent methodological advances provide new tools for rapid profiling of tRNA modifications and have led to discoveries of novel modifications and their regulation. Here, we provide an overview of the techniques for investigating tRNA modifications and of the expanding knowledge of their chemistry and regulation.
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Affiliation(s)
- Satoshi Kimura
- Division of Infectious Diseases, Brigham and Women's Hospital, United States; Department of Microbiology, Harvard Medical School, United States; Howard Hughes Medical Institute, United States.
| | - Veerasak Srisuknimit
- Division of Infectious Diseases, Brigham and Women's Hospital, United States; Department of Microbiology, Harvard Medical School, United States; Howard Hughes Medical Institute, United States
| | - Matthew K Waldor
- Division of Infectious Diseases, Brigham and Women's Hospital, United States; Department of Microbiology, Harvard Medical School, United States; Howard Hughes Medical Institute, United States.
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25
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26
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Cheng HP, Yang XH, Lan L, Xie LJ, Chen C, Liu C, Chu J, Li ZY, Liu L, Zhang TQ, Luo DQ, Cheng L. Chemical Deprenylation of N 6 -Isopentenyladenosine (i 6 A) RNA. Angew Chem Int Ed Engl 2020; 59:10645-10650. [PMID: 32198805 DOI: 10.1002/anie.202003360] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 03/20/2020] [Indexed: 12/19/2022]
Abstract
N6 -isopentenyladenosine (i6 A) is an RNA modification found in cytokinins, which regulate plant growth/differentiation, and a subset of tRNAs, where it improves the efficiency and accuracy of translation. The installation and removal of this modification is mediated by prenyltransferases and cytokinin oxidases, and a chemical approach to selective deprenylation of i6 A has not been developed. We show that a selected group of oxoammonium cations function as artificial deprenylases to promote highly selective deprenylation of i6 A in nucleosides, oligonucleotides, and live cells. Importantly, other epigenetic modifications, amino acid residues, and natural products were not affected. Moreover, a significant phenotype difference in the Arabidopsis thaliana shoot and root development was observed with incubation of the cation. These results establish these small organic molecules as direct chemical regulators/artificial deprenylases of i6 A.
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Affiliation(s)
- Hou-Ping Cheng
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao-Hui Yang
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, College of Life Science, Hebei University, Hebei, 071002, China
| | - Ling Lan
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li-Jun Xie
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chuan Chen
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, College of Life Science, Hebei University, Hebei, 071002, China
| | - Cuimei Liu
- National Centre for Plant Gene Research (Beijing), Innovation Academy for Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jinfang Chu
- National Centre for Plant Gene Research (Beijing), Innovation Academy for Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhi-Yan Li
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Li Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tian-Qi Zhang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences, Shanghai, 200032, China
| | - Du-Qiang Luo
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, College of Life Science, Hebei University, Hebei, 071002, China
| | - Liang Cheng
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
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27
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Wang CA, Liu C, Szostak M. N-Acyl-5,5-Dimethylhydantoins: Mild Acyl-Transfer Reagents for the Synthesis of Ketones Using Pd–PEPPSI or Pd/Phosphine Catalysts. Org Process Res Dev 2020. [DOI: 10.1021/acs.oprd.0c00054] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Chang-An Wang
- College of Chemistry and Chemical Engineering, Taishan University, Tai’an, Shandong 271000, China
- Department of Chemistry, Rutgers University, 73 Warren Street, Newark, New Jersey 07102, United States
| | - Chengwei Liu
- Department of Chemistry, Rutgers University, 73 Warren Street, Newark, New Jersey 07102, United States
| | - Michal Szostak
- Department of Chemistry, Rutgers University, 73 Warren Street, Newark, New Jersey 07102, United States
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28
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Debiec K, Matuszewski M, Podskoczyj K, Leszczynska G, Sochacka E. Chemical Synthesis of Oligoribonucleotide (ASL of tRNA Lys T. brucei) Containing a Recently Discovered Cyclic Form of 2-Methylthio-N 6 -threonylcarbamoyladenosine (ms 2 ct 6 A). Chemistry 2019; 25:13309-13317. [PMID: 31328310 DOI: 10.1002/chem.201902411] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 07/16/2019] [Indexed: 01/25/2023]
Abstract
The synthesis of the protected form of 2-methylthio-N6 -threonylcarbamoyl adenosine (ms2 t6 A) was developed starting from adenosine or guanosine by using the optimized carbamate method and, for the first time, an isocyanate route. The hypermodified nucleoside was subsequently transformed into the protected ms2 t6 A-phosphoramidite monomer and used in a large-scale synthesis of the precursor 17nt ms2 t6 A-oligonucleotide (the anticodon stem and loop fragment of tRNALys from T. brucei). Finally, stereochemically secure ms2 t6 A→ms2 ct6 A cyclization at the oligonucleotide level efficiently afforded a tRNA fragment bearing the ms2 ct6 A unit. The applied post-synthetic approach provides two sequentially homologous ms2 t6 A- and ms2 ct6 A-oligonucleotides that are suitable for further comparative structure-activity relationship studies.
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Affiliation(s)
- Katarzyna Debiec
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Łódź, Poland
| | - Michal Matuszewski
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Łódź, Poland
| | - Karolina Podskoczyj
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Łódź, Poland
| | - Grazyna Leszczynska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Łódź, Poland
| | - Elzbieta Sochacka
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Łódź, Poland
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29
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Szostak R, Liu C, Lalancette R, Szostak M. Twisted N-Acyl-hydantoins: Rotationally Inverted Urea-Imides of Relevance in N-C(O) Cross-coupling. J Org Chem 2018; 83:14676-14682. [PMID: 30352152 DOI: 10.1021/acs.joc.8b02691] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We report a combined structural and computational study on the properties of twisted acyclic hydantoins. These compounds feature cyclic urea-imide moiety that is widely found in bioactive compounds and is structurally related to the classic bridged hydantoins proposed by Smissman more than 50 years ago. We demonstrate that C to N-substitution of the imide moiety in the succinimide ring to give hydantoin results in one of the most distorted acyclic amide bonds reported to date. The energetic properties of twisted acyclic hydantoins with respect to structures, resonance energies, barriers to rotation, and proton affinities are discussed. The energetic and structural properties of twisted acyclic hydantoins described provide a benchmark to facilitate the development of twisted amides based on the biorelevant cyclic urea-imide scaffold.
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Affiliation(s)
- Roman Szostak
- Department of Chemistry , Wroclaw University , F. Joliot-Curie 14 , Wroclaw 50-383 , Poland
| | - Chengwei Liu
- Department of Chemistry , Rutgers University , 73 Warren Street , Newark , New Jersey 07102 , United States
| | - Roger Lalancette
- Department of Chemistry , Rutgers University , 73 Warren Street , Newark , New Jersey 07102 , United States
| | - Michal Szostak
- Department of Chemistry , Rutgers University , 73 Warren Street , Newark , New Jersey 07102 , United States
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30
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Detection of ribonucleoside modifications by liquid chromatography coupled with mass spectrometry. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:280-290. [PMID: 30414470 DOI: 10.1016/j.bbagrm.2018.10.012] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 09/20/2018] [Accepted: 10/27/2018] [Indexed: 12/21/2022]
Abstract
A small set of ribonucleoside modifications have been found in different regions of mRNA including the open reading frame. Accurate detection of these specific modifications is critical to understanding their modulatory roles in facilitating mRNA maturation, translation and degradation. While transcriptome-wide next-generation sequencing (NGS) techniques could provide exhaustive information about the sites of one specific or class of modifications at a time, recent investigations strongly indicate cautionary interpretation due to the appearance of false positives. Therefore, it is suggested that NGS-based modification data can only be treated as predicted sites and their existence need to be validated by orthogonal methods. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is an analytical technique that can yield accurate and reproducible information about the qualitative and quantitative characteristics of ribonucleoside modifications. Here, we review the recent advancements in LC-MS/MS technology that could help in securing accurate, gold-standard quality information about the resident post-transcriptional modifications of mRNA.
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31
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Kumbhar NM, Gopal JS. Structural significance of hypermodified nucleoside 5-carboxymethylaminomethyluridine (cmnm 5U) from 'wobble' (34th) position of mitochondrial tRNAs: Molecular modeling and Markov state model studies. J Mol Graph Model 2018; 86:66-83. [PMID: 30336453 DOI: 10.1016/j.jmgm.2018.10.004] [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: 03/06/2018] [Revised: 10/02/2018] [Accepted: 10/04/2018] [Indexed: 11/28/2022]
Abstract
A quantum chemical semi-empirical RM1 approach was used to deduce the structural role of hypermodified nucleoside 5-carboxymethylaminomethyluridine 5'-monophosphate (pcmnm5U) from 'wobble' (34th) position of mitochondrial tRNAs. The energetically preferred pcmnm5U(34) adopted a 'skew' conformation for C5-substituted side chain (-CH2-NH2+-CH2-COO-) moiety that orient towards the 5'-ribose-phosphate backbone, which support 'anti' orientation of glycosyl (χ34) torsion angle. Preferred conformation of pcmnm5U(34) was stabilized by O(4) … HC(10), O1P⋯HN(11), O(15) … HN(11), O(15) … HC(10), O4' … HC(6) and O(2) … HC2' hydrogen bonding interactions. The high flexibility of side chain moiety displayed different structural properties for pcmnm5U(34). Three different conformations of pcmnm5U(34) were observed in molecular dynamics simulations and Markov state model studies. The unmodified uracil revealed 'syn' and 'anti' orientations for glycosyl (χ34) torsion angle that substantiate the role of "-CH2-NH2+-CH2-COO-" moiety in maintaining the 'anti' orientation of pcmnm5U(34). The preferred conformation of pcmnm5U(34) helps to recognize Guanosine more proficiently than Adenosine from the third position of codons. The role of pcmnm5U(34) in tRNA biogenesis paves the way to understand its structural significance in usual mitochondrial metabolism and respiration.
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Affiliation(s)
- Navanath M Kumbhar
- Garware Research Centre, Department of Chemistry, Savitribai Phule Pune University (Formerly University of Pune), Pune, 411007, India.
| | - Janhavi S Gopal
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University (Formerly University of Pune), Pune, 411007, India
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32
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Jora M, Burns AP, Ross RL, Lobue PA, Zhao R, Palumbo CM, Beal PA, Addepalli B, Limbach PA. Differentiating Positional Isomers of Nucleoside Modifications by Higher-Energy Collisional Dissociation Mass Spectrometry (HCD MS). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1745-1756. [PMID: 29949056 PMCID: PMC6062210 DOI: 10.1007/s13361-018-1999-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 05/22/2018] [Accepted: 05/24/2018] [Indexed: 05/03/2023]
Abstract
The analytical identification of positional isomers (e.g., 3-, N4-, 5-methylcytidine) within the > 160 different post-transcriptional modifications found in RNA can be challenging. Conventional liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) approaches rely on chromatographic separation for accurate identification because the collision-induced dissociation (CID) mass spectra of these isomers nearly exclusively yield identical nucleobase ions (BH2+) from the same molecular ion (MH+). Here, we have explored higher-energy collisional dissociation (HCD) as an alternative fragmentation technique to generate more informative product ions that can be used to differentiate positional isomers. LC-MS/MS of modified nucleosides characterized using HCD led to the creation of structure- and HCD energy-specific fragmentation patterns that generated unique fingerprints, which can be used to identify individual positional isomers even when they cannot be separated chromatographically. While particularly useful for identifying positional isomers, the fingerprinting capabilities enabled by HCD also offer the potential to generate HPLC-independent spectral libraries for the rapid analysis of modified ribonucleosides. Graphical Abstract ᅟ.
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Affiliation(s)
- Manasses Jora
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Andrew P Burns
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Robert L Ross
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Peter A Lobue
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Ruoxia Zhao
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Cody M Palumbo
- Department of Chemistry, University of California, Davis, California, 95616, USA
| | - Peter A Beal
- Department of Chemistry, University of California, Davis, California, 95616, USA
| | - Balasubrahmanyam Addepalli
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Patrick A Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, 45221, USA.
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33
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Lin H, Miyauchi K, Harada T, Okita R, Takeshita E, Komaki H, Fujioka K, Yagasaki H, Goto YI, Yanaka K, Nakagawa S, Sakaguchi Y, Suzuki T. CO 2-sensitive tRNA modification associated with human mitochondrial disease. Nat Commun 2018; 9:1875. [PMID: 29760464 PMCID: PMC5951830 DOI: 10.1038/s41467-018-04250-4] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 04/16/2018] [Indexed: 12/21/2022] Open
Abstract
It has been generally thought that tRNA modifications are stable and static, and their frequencies are rarely regulated. N6-threonylcarbamoyladenosine (t6A) occurs at position 37 of five mitochondrial (mt-)tRNA species. We show that YRDC and OSGEPL1 are responsible for t6A37 formation, utilizing L-threonine, ATP, and CO2/bicarbonate as substrates. OSGEPL1-knockout cells exhibit respiratory defects and reduced mitochondrial translation. We find low level of t6A37 in mutant mt-tRNA isolated from the MERRF-like patient’s cells, indicating that lack of t6A37 results in pathological consequences. Kinetic measurements of t6A37 formation reveal that the Km value of CO2/bicarbonate is extremely high (31 mM), suggesting that CO2/bicarbonate is a rate-limiting factor for t6A37 formation. Consistent with this, we observe a low frequency of t6A37 in mt-tRNAs isolated from human cells cultured without bicarbonate. These findings indicate that t6A37 is regulated by sensing intracellular CO2/bicarbonate concentration, implying that mitochondrial translation is modulated in a codon-specific manner under physiological conditions. Transfer RNA modifications play critical roles in protein synthesis. Here the authors reveal the t6A37 tRNA modification is dynamically regulated by sensing intracellular CO2 concentration in mitochondria, implying metabolic regulation of protein synthesis.
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Affiliation(s)
- Huan Lin
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Kenjyo Miyauchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Tai Harada
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Ryo Okita
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Eri Takeshita
- Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, 4-1-1 Ogawahigashi, Kodaira, Tokyo, 187-8502, Japan.,Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, 4-1-1 Ogawahigashi, Kodaira, Tokyo, 187-8502, Japan
| | - Hirofumi Komaki
- Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, 4-1-1 Ogawahigashi, Kodaira, Tokyo, 187-8502, Japan.,Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, 4-1-1 Ogawahigashi, Kodaira, Tokyo, 187-8502, Japan
| | - Kaoru Fujioka
- Department of Pediatrics, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi, Yamanashi, 409-3898, Japan
| | - Hideki Yagasaki
- Department of Pediatrics, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi, Yamanashi, 409-3898, Japan
| | - Yu-Ichi Goto
- Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, 4-1-1 Ogawahigashi, Kodaira, Tokyo, 187-8502, Japan.,Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, 4-1-1 Ogawahigashi, Kodaira, Tokyo, 187-8502, Japan.,Medical Genome Center, National Center of Neurology and Psychiatry, 4-1-1 Ogawahigashi, Kodaira, Tokyo, 187-8502, Japan
| | - Kaori Yanaka
- RNA Biology Laboratory, RIKEN Advanced Research Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Shinichi Nakagawa
- RNA Biology Laboratory, RIKEN Advanced Research Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.,RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12-jo Nishi 6-chome, Kita-ku, Sapporo, 060-0812, Japan
| | - Yuriko Sakaguchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.
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34
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Dal Magro C, Keller P, Kotter A, Werner S, Duarte V, Marchand V, Ignarski M, Freiwald A, Müller RU, Dieterich C, Motorin Y, Butter F, Atta M, Helm M. Die stark wachsende chemische Vielfalt der RNA-Modifikationen enthält eine Thioacetalstruktur. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201713188] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Christina Dal Magro
- Institut für Pharmazie und Biochemie; Johannes Gutenberg-Universität Mainz; Staudinger Weg 5 55128 Mainz Deutschland
| | - Patrick Keller
- Institut für Pharmazie und Biochemie; Johannes Gutenberg-Universität Mainz; Staudinger Weg 5 55128 Mainz Deutschland
| | - Annika Kotter
- Institut für Pharmazie und Biochemie; Johannes Gutenberg-Universität Mainz; Staudinger Weg 5 55128 Mainz Deutschland
| | - Stephan Werner
- Institut für Pharmazie und Biochemie; Johannes Gutenberg-Universität Mainz; Staudinger Weg 5 55128 Mainz Deutschland
| | - Victor Duarte
- Laboratoire de Chimie et Biologie des Métaux; Université Grenoble Alpes, CEA/BIG, CNRS; 17 rue des martyrs 38000 Grenoble Frankreich
| | - Virginie Marchand
- Next-Generation Sequencing Core Facility, FR3209 Bioingénierie Moléculaire Cellulaire et Thérapeutique, CNRS; Lorraine University; 54505 Vandoeuvre-les-Nancy Frankreich
| | - Michael Ignarski
- Department II of Internal Medicine and Center for Molecular Medicine; Universität zu Köln; Kerpener Straße 62 50937 Cologne Deutschland
| | - Anja Freiwald
- Institute of Molecular Biology (IMB); Ackermannweg 4 55128 Mainz Deutschland
| | - Roman-Ulrich Müller
- Department II of Internal Medicine and Center for Molecular Medicine; Universität zu Köln; Kerpener Straße 62 50937 Cologne Deutschland
| | - Christoph Dieterich
- Deutsches Zentrum für Herz-Kreislauf-Forschung e. V. (DZHK); Universitätsklinikum Heidelberg; Im Neuenheimer Feld 669 69120 Heidelberg Deutschland
| | - Yuri Motorin
- Laboratoire Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA) UMR7365 CNRS-UL; BioPôle de l'Université de Lorraine Campus Biologie-Santé; 9 avenue de la Forêt de Haye, CS 50184 54505 Vandoeuvre-les-Nancy Frankreich
| | - Falk Butter
- Institute of Molecular Biology (IMB); Ackermannweg 4 55128 Mainz Deutschland
| | - Mohamed Atta
- Laboratoire de Chimie et Biologie des Métaux; Université Grenoble Alpes, CEA/BIG, CNRS; 17 rue des martyrs 38000 Grenoble Frankreich
| | - Mark Helm
- Institut für Pharmazie und Biochemie; Johannes Gutenberg-Universität Mainz; Staudinger Weg 5 55128 Mainz Deutschland
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35
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Dal Magro C, Keller P, Kotter A, Werner S, Duarte V, Marchand V, Ignarski M, Freiwald A, Müller RU, Dieterich C, Motorin Y, Butter F, Atta M, Helm M. A Vastly Increased Chemical Variety of RNA Modifications Containing a Thioacetal Structure. Angew Chem Int Ed Engl 2018; 57:7893-7897. [DOI: 10.1002/anie.201713188] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Indexed: 12/19/2022]
Affiliation(s)
- Christina Dal Magro
- Institute of Pharmacy and Biochemistry; Johannes Gutenberg-University Mainz; Staudingerweg 5 55128 Mainz Germany
| | - Patrick Keller
- Institute of Pharmacy and Biochemistry; Johannes Gutenberg-University Mainz; Staudingerweg 5 55128 Mainz Germany
| | - Annika Kotter
- Institute of Pharmacy and Biochemistry; Johannes Gutenberg-University Mainz; Staudingerweg 5 55128 Mainz Germany
| | - Stephan Werner
- Institute of Pharmacy and Biochemistry; Johannes Gutenberg-University Mainz; Staudingerweg 5 55128 Mainz Germany
| | - Victor Duarte
- Laboratoire de Chimie et Biologie des Métaux; Université Grenoble Alpes, CEA/BIG; CNRS; 17 rue des martyrs 38000 Grenoble France
| | - Virginie Marchand
- Next-Generation Sequencing Core Facility, FR3209 Bioingénierie Moléculaire Cellulaire et Thérapeutique, CNRS; Lorraine University; 54505 Vandoeuvre-les-Nancy France
| | - Michael Ignarski
- Department II of Internal Medicine and Center for Molecular Medicine; University of Cologne; Kerpener Strasse 62 50937 Cologne Germany
| | - Anja Freiwald
- Institute of Molecular Biology (IMB); Ackermannweg 4 55128 Mainz Germany
| | - Roman-Ulrich Müller
- Department II of Internal Medicine and Center for Molecular Medicine; University of Cologne; Kerpener Strasse 62 50937 Cologne Germany
| | - Christoph Dieterich
- German Center for Cardiovascular Research (DZHK); University Hospital Heidelberg; Im Neuenheimer Feld 669 69120 Heidelberg Germany
| | - Yuri Motorin
- Laboratoire Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA) UMR7365 CNRS-UL; BioPôle de l'Université de Lorraine Campus Biologie-Santé; 9 avenue de la Forêt de Haye, CS 50184 54505 Vandoeuvre-les-Nancy France
| | - Falk Butter
- Institute of Molecular Biology (IMB); Ackermannweg 4 55128 Mainz Germany
| | - Mohamed Atta
- Laboratoire de Chimie et Biologie des Métaux; Université Grenoble Alpes, CEA/BIG; CNRS; 17 rue des martyrs 38000 Grenoble France
| | - Mark Helm
- Institute of Pharmacy and Biochemistry; Johannes Gutenberg-University Mainz; Staudingerweg 5 55128 Mainz Germany
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36
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Matuszewski M, Debiec K, Sochacka E. Efficient conversion of N 6-threonylcarbamoyladenosine (t 6A) into a tRNA native hydantoin cyclic form (ct 6A) performed at nucleoside and oligoribonucleotide levels. Chem Commun (Camb) 2018; 53:7945-7948. [PMID: 28657616 DOI: 10.1039/c7cc03560h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A t6A nucleoside was efficiently and stereospecifically transformed into a hydantoin cyclic form of N6-l-threonylcarbamoyladenosine (ct6A) by the use of polymer bounded carbodiimide (EDC-P) and HOBt. The procedure was successfully applied for a post-synthetic conversion of t6A-containing RNA 17-mers (of the sequences of anticodon stem and loop (ASL) fragments of S. pombe tRNAi and E. coli tRNALys) into the products bearing the ct6A unit.
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Affiliation(s)
- Michal Matuszewski
- Institute of Organic Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland.
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Nagao A, Ohara M, Miyauchi K, Yokobori SI, Yamagishi A, Watanabe K, Suzuki T. Hydroxylation of a conserved tRNA modification establishes non-universal genetic code in echinoderm mitochondria. Nat Struct Mol Biol 2017; 24:778-782. [PMID: 28783151 DOI: 10.1038/nsmb.3449] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 07/11/2017] [Indexed: 12/13/2022]
Abstract
The genetic code is not frozen but still evolving, which can result in the acquisition of 'dialectal' codons that deviate from the universal genetic code. RNA modifications in the anticodon region of tRNAs play a critical role in establishing such non-universal genetic codes. In echinoderm mitochondria, the AAA codon specifies asparagine instead of lysine. By analyzing mitochondrial (mt-) tRNALys isolated from the sea urchin (Mesocentrotus nudus), we discovered a novel modified nucleoside, hydroxy-N6-threonylcarbamoyladenosine (ht6A), 3' adjacent to the anticodon (position 37). Biochemical analysis revealed that ht6A37 has the ability to prevent mt-tRNALys from misreading AAA as lysine, thereby indicating that hydroxylation of N6-threonylcarbamoyladenosine (t6A) contributes to the establishment of the non-universal genetic code in echinoderm mitochondria.
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Affiliation(s)
- Asuteka Nagao
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo, Japan
| | - Mitsuhiro Ohara
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo, Japan
| | - Kenjyo Miyauchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo, Japan
| | - Shin-Ichi Yokobori
- Department of Applied Life Sciences, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Akihiko Yamagishi
- Department of Applied Life Sciences, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Kimitsuna Watanabe
- Department of Applied Life Sciences, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo, Japan
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Zheng C, Black KA, Dos Santos PC. Diverse Mechanisms of Sulfur Decoration in Bacterial tRNA and Their Cellular Functions. Biomolecules 2017; 7:biom7010033. [PMID: 28327539 PMCID: PMC5372745 DOI: 10.3390/biom7010033] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 03/10/2017] [Accepted: 03/16/2017] [Indexed: 01/01/2023] Open
Abstract
Sulfur-containing transfer ribonucleic acids (tRNAs) are ubiquitous biomolecules found in all organisms that possess a variety of functions. For decades, their roles in processes such as translation, structural stability, and cellular protection have been elucidated and appreciated. These thionucleosides are found in all types of bacteria; however, their biosynthetic pathways are distinct among different groups of bacteria. Considering that many of the thio-tRNA biosynthetic enzymes are absent in Gram-positive bacteria, recent studies have addressed how sulfur trafficking is regulated in these prokaryotic species. Interestingly, a novel proposal has been given for interplay among thionucleosides and the biosynthesis of other thiocofactors, through participation of shared-enzyme intermediates, the functions of which are impacted by the availability of substrate as well as metabolic demand of thiocofactors. This review describes the occurrence of thio-modifications in bacterial tRNA and current methods for detection of these modifications that have enabled studies on the biosynthesis and functions of S-containing tRNA across bacteria. It provides insight into potential modes of regulation and potential evolutionary events responsible for divergence in sulfur metabolism among prokaryotes.
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Affiliation(s)
- Chenkang Zheng
- Department of Chemistry, Wake Forest University, Winston-Salem, NC 27101, USA.
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Kang BI, Miyauchi K, Matuszewski M, D'Almeida GS, Rubio M, Alfonzo JD, Inoue K, Sakaguchi Y, Suzuki T, Sochacka E, Suzuki T. Identification of 2-methylthio cyclic N6-threonylcarbamoyladenosine (ms2ct6A) as a novel RNA modification at position 37 of tRNAs. Nucleic Acids Res 2017; 45:2124-2136. [PMID: 27913733 PMCID: PMC5389704 DOI: 10.1093/nar/gkw1120] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 11/09/2016] [Indexed: 02/01/2023] Open
Abstract
Transfer RNA modifications play pivotal roles in protein synthesis. N6-threonylcarbamoyladenosine (t6A) and its derivatives are modifications found at position 37, 3΄-adjacent to the anticodon, in tRNAs responsible for ANN codons. These modifications are universally conserved in all domains of life. t6A and its derivatives have pleiotropic functions in protein synthesis including aminoacylation, decoding and translocation. We previously discovered a cyclic form of t6A (ct6A) as a chemically labile derivative of t6A in tRNAs from bacteria, fungi, plants and protists. Here, we report 2-methylthio cyclic t6A (ms2ct6A), a novel derivative of ct6A found in tRNAs from Bacillus subtilis, plants and Trypanosoma brucei. In B. subtilis and T. brucei, ms2ct6A disappeared and remained to be ms2t6A and ct6A by depletion of tcdA and mtaB homologs, respectively, demonstrating that TcdA and MtaB are responsible for biogenesis of ms2ct6A.
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Affiliation(s)
- Byeong-il Kang
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan
| | - Kenjyo Miyauchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan
| | - Michal Matuszewski
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Lodz 90-924, Poland
| | - Gabriel Silveira D'Almeida
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Mary Anne T. Rubio
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Juan D. Alfonzo
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Kazuki Inoue
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan
| | - Yuriko Sakaguchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan
| | - Takeo Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan
| | - Elzbieta Sochacka
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Lodz 90-924, Poland
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan
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