1
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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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2
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Abstract
The study of eukaryotic tRNA processing has given rise to an explosion of new information and insights in the last several years. We now have unprecedented knowledge of each step in the tRNA processing pathway, revealing unexpected twists in biochemical pathways, multiple new connections with regulatory pathways, and numerous biological effects of defects in processing steps that have profound consequences throughout eukaryotes, leading to growth phenotypes in the yeast Saccharomyces cerevisiae and to neurological and other disorders in humans. This review highlights seminal new results within the pathways that comprise the life of a tRNA, from its birth after transcription until its death by decay. We focus on new findings and revelations in each step of the pathway including the end-processing and splicing steps, many of the numerous modifications throughout the main body and anticodon loop of tRNA that are so crucial for tRNA function, the intricate tRNA trafficking pathways, and the quality control decay pathways, as well as the biogenesis and biology of tRNA-derived fragments. We also describe the many interactions of these pathways with signaling and other pathways in the cell.
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Affiliation(s)
- Eric M Phizicky
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York 14642, USA
| | - Anita K Hopper
- Department of Molecular Genetics and Center for RNA Biology, Ohio State University, Columbus, Ohio 43235, USA
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3
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A paralog of Pcc1 is the fifth core subunit of the KEOPS tRNA-modifying complex in Archaea. Nat Commun 2023; 14:526. [PMID: 36720870 PMCID: PMC9889334 DOI: 10.1038/s41467-023-36210-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 01/20/2023] [Indexed: 02/02/2023] Open
Abstract
In Archaea and Eukaryotes, the synthesis of a universal tRNA modification, N6-threonyl-carbamoyl adenosine (t6A), is catalyzed by the KEOPS complex composed of Kae1, Bud32, Cgi121, and Pcc1. A fifth subunit, Gon7, is found only in Fungi and Metazoa. Here, we identify and characterize a fifth KEOPS subunit in Archaea. This protein, dubbed Pcc2, is a paralog of Pcc1 and is widely conserved in Archaea. Pcc1 and Pcc2 form a heterodimer in solution, and show modest sequence conservation but very high structural similarity. The five-subunit archaeal KEOPS does not form dimers but retains robust tRNA binding and t6A synthetic activity. Pcc2 can substitute for Pcc1 but the resulting KEOPS complex is inactive, suggesting a distinct function for the two paralogs. Comparative sequence and structure analyses point to a possible evolutionary link between archaeal Pcc2 and eukaryotic Gon7. Our work indicates that Pcc2 regulates the oligomeric state of the KEOPS complex, a feature that seems to be conserved from Archaea to Eukaryotes.
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4
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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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5
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Ziemkiewicz K, Warminski M, Wojcik R, Kowalska J, Jemielity J. Quick Access to Nucleobase-Modified Phosphoramidites for the Synthesis of Oligoribonucleotides Containing Post-Transcriptional Modifications and Epitranscriptomic Marks. J Org Chem 2022; 87:10333-10348. [PMID: 35857285 PMCID: PMC9361293 DOI: 10.1021/acs.joc.2c01390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Herein, we report a straightforward one-step procedure
for modifying N-nucleophilic groups in the nucleobases
of commercially
available nucleoside phosphoramidites. This method involves the deprotonation
of amide groups under phase-transfer conditions and subsequent reaction
with electrophilic molecules such as alkyl halides or organic isocyanates.
Using this approach, we obtained 10 different classes of modified
nucleoside phosphoramidites suitable for the synthesis of oligonucleotides,
including several noncanonical nucleotides found in natural RNA or
DNA (e.g., m6A, i6A, m1A, g6A, m3C, m4C, m3U, m1G,
and m2G). Such modification of nucleobases is a common
mechanism for post-transcriptional regulation of RNA stability and
translational activity in various organisms. To better understand
this process, relevant cellular recognition partners (e.g., proteins)
must be identified and characterized. However, this step has been
impeded by limited access to molecular tools containing such modified
nucleotides.
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Affiliation(s)
- Kamil Ziemkiewicz
- Centre of New Technologies, University of Warsaw, Banacha 2c, Warsaw 02-097, Poland
| | - Marcin Warminski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, Warsaw 02-093, Poland
| | - Radoslaw Wojcik
- Centre of New Technologies, University of Warsaw, Banacha 2c, Warsaw 02-097, Poland
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, Warsaw 02-093, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, Banacha 2c, Warsaw 02-097, Poland
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6
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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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7
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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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8
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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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9
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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: 261] [Impact Index Per Article: 87.0] [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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10
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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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11
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Zhou JB, Wang Y, Zeng QY, Meng SX, Wang ED, Zhou XL. Molecular basis for t6A modification in human mitochondria. Nucleic Acids Res 2020; 48:3181-3194. [PMID: 32047918 PMCID: PMC7102964 DOI: 10.1093/nar/gkaa093] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 01/31/2020] [Accepted: 02/05/2020] [Indexed: 12/27/2022] Open
Abstract
N6-Threonylcarbamoyladenosine (t6A) is a universal tRNA modification essential for translational accuracy and fidelity. In human mitochondria, YrdC synthesises an l-threonylcarbamoyl adenylate (TC-AMP) intermediate, and OSGEPL1 transfers the TC-moiety to five tRNAs, including human mitochondrial tRNAThr (hmtRNAThr). Mutation of hmtRNAs, YrdC and OSGEPL1, affecting efficient t6A modification, has been implicated in various human diseases. However, little is known about the tRNA recognition mechanism in t6A formation in human mitochondria. Herein, we showed that OSGEPL1 is a monomer and is unique in utilising C34 as an anti-determinant by studying the contributions of individual bases in the anticodon loop of hmtRNAThr to t6A modification. OSGEPL1 activity was greatly enhanced by introducing G38A in hmtRNAIle or the A28:U42 base pair in a chimeric tRNA containing the anticodon stem of hmtRNASer(AGY), suggesting that sequences of specific hmtRNAs are fine-tuned for different modification levels. Moreover, using purified OSGEPL1, we identified multiple acetylation sites, and OSGEPL1 activity was readily affected by acetylation via multiple mechanisms in vitro and in vivo. Collectively, we systematically elucidated the nucleotide requirement in the anticodon loop of hmtRNAs, and revealed mechanisms involving tRNA sequence optimisation and post-translational protein modification that determine t6A modification levels.
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Affiliation(s)
- Jing-Bo Zhou
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Yong Wang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China.,School of Life Science and Technology, ShanghaiTech University, 100 Hai Ke Road, Shanghai 201210, China
| | - Qi-Yu Zeng
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Shi-Xin Meng
- Biology Department, College of Science, Purdue University, 150 N. University St, West Lafayette, IN 47907, USA
| | - En-Duo Wang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China.,School of Life Science and Technology, ShanghaiTech University, 100 Hai Ke Road, Shanghai 201210, China
| | - Xiao-Long Zhou
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
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12
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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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13
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Chatterjee K, Nostramo RT, Wan Y, Hopper AK. tRNA dynamics between the nucleus, cytoplasm and mitochondrial surface: Location, location, location. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2018; 1861:373-386. [PMID: 29191733 PMCID: PMC5882565 DOI: 10.1016/j.bbagrm.2017.11.007] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 11/19/2017] [Accepted: 11/23/2017] [Indexed: 01/20/2023]
Abstract
Although tRNAs participate in the essential function of protein translation in the cytoplasm, tRNA transcription and numerous processing steps occur in the nucleus. This subcellular separation between tRNA biogenesis and function requires that tRNAs be efficiently delivered to the cytoplasm in a step termed "primary tRNA nuclear export". Surprisingly, tRNA nuclear-cytoplasmic traffic is not unidirectional, but, rather, movement is bidirectional. Cytoplasmic tRNAs are imported back to the nucleus by the "tRNA retrograde nuclear import" step which is conserved from budding yeast to vertebrate cells and has been hijacked by viruses, such as HIV, for nuclear import of the viral reverse transcription complex in human cells. Under appropriate environmental conditions cytoplasmic tRNAs that have been imported into the nucleus return to the cytoplasm via the 3rd nuclear-cytoplasmic shuttling step termed "tRNA nuclear re-export", that again is conserved from budding yeast to vertebrate cells. We describe the 3 steps of tRNA nuclear-cytoplasmic movements and their regulation. There are multiple tRNA nuclear export and import pathways. The different tRNA nuclear exporters appear to possess substrate specificity leading to the tantalizing possibility that the cellular proteome may be regulated at the level of tRNA nuclear export. Moreover, in some organisms, such as budding yeast, the pre-tRNA splicing heterotetrameric endonuclease (SEN), which removes introns from pre-tRNAs, resides on the cytoplasmic surface of the mitochondria. Therefore, we also describe the localization of the SEN complex to mitochondria and splicing of pre-tRNA on mitochondria, which occurs prior to the participation of tRNAs in protein translation. This article is part of a Special Issue entitled: SI: Regulation of tRNA synthesis and modification in physiological conditions and disease edited by Dr. Boguta Magdalena.
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Affiliation(s)
- Kunal Chatterjee
- The Ohio State University Comprehensive Cancer Research Center, United States; Department of Molecular Genetics, The Ohio State University, United States; Center for RNA Biology, The Ohio State University, United States
| | - Regina T Nostramo
- Department of Molecular Genetics, The Ohio State University, United States; Center for RNA Biology, The Ohio State University, United States
| | - Yao Wan
- The Ohio State University Comprehensive Cancer Research Center, United States; Department of Molecular Genetics, The Ohio State University, United States; Center for RNA Biology, The Ohio State University, United States
| | - Anita K Hopper
- Department of Molecular Genetics, The Ohio State University, United States; Center for RNA Biology, The Ohio State University, United States.
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14
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Function and Biosynthesis of the Universal tRNA Modification N6-Threonylcarbamoyl-Adenosine. ACTA ACUST UNITED AC 2017. [DOI: 10.1007/978-3-319-65795-0_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
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15
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Matuszewski M, Wojciechowski J, Miyauchi K, Gdaniec Z, Wolf WM, Suzuki T, Sochacka E. A hydantoin isoform of cyclic N6-threonylcarbamoyladenosine (ct6A) is present in tRNAs. Nucleic Acids Res 2017; 45:2137-2149. [PMID: 27913732 PMCID: PMC5389693 DOI: 10.1093/nar/gkw1189] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 11/25/2016] [Indexed: 02/06/2023] Open
Abstract
N6-Threonylcarbamoyladenosine (t6A) and its derivatives are universally conserved modified nucleosides found at position 37, 3΄ adjacent to the anticodon in tRNAs responsible for ANN codons. These modifications have pleiotropic functions of tRNAs in decoding and protein synthesis. In certain species of bacteria, fungi, plants and protists, t6A is further modified to the cyclic t6A (ct6A) via dehydration catalyzed by TcdA. This additional modification is involved in efficient decoding of tRNALys. Previous work indicated that the chemical structure of ct6A is a cyclic active ester with an oxazolone ring. In this study, we solved the crystal structure of chemically synthesized ct6A nucleoside. Unexpectedly, we found that the ct6A adopted a hydantoin isoform rather than an oxazolone isoform, and further showed that the hydantoin isoform of ct6A was actually present in Escherichia coli tRNAs. In addition, we observed that hydantoin ct6A is susceptible to epimerization under mild alkaline conditions, warning us to avoid conventional deacylation of tRNAs. A hallmark structural feature of this isoform is the twisted arrangement of the hydantoin and adenine rings. Functional roles of ct6A37 in tRNAs should be reconsidered.
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Affiliation(s)
- Michal Matuszewski
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Jakub Wojciechowski
- Institute of General and Ecological Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Kenjyo Miyauchi
- Department of Chemistry and Biotechnology, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Zofia Gdaniec
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Wojciech M Wolf
- Institute of General and Ecological Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Elzbieta Sochacka
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
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16
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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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17
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Wan LCK, Pillon MC, Thevakumaran N, Sun Y, Chakrabartty A, Guarné A, Kurinov I, Durocher D, Sicheri F. Structural and functional characterization of KEOPS dimerization by Pcc1 and its role in t6A biosynthesis. Nucleic Acids Res 2016; 44:6971-80. [PMID: 27302132 PMCID: PMC5001605 DOI: 10.1093/nar/gkw542] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 06/03/2016] [Indexed: 11/20/2022] Open
Abstract
KEOPS is an ancient protein complex required for the biosynthesis of N6-threonylcarbamoyladenosine (t6A), a universally conserved tRNA modification found on all ANN-codon recognizing tRNAs. KEOPS consist minimally of four essential subunits, namely the proteins Kae1, Bud32, Cgi121 and Pcc1, with yeast possessing the fifth essential subunit Gon7. Bud32, Cgi121, Pcc1 and Gon7 appear to have evolved to regulate the central t6A biosynthesis function of Kae1, but their precise function and mechanism of action remains unclear. Pcc1, in particular, binds directly to Kae1 and by virtue of its ability to form dimers in solution and in crystals, Pcc1 was inferred to function as a dimerization module for Kae1 and therefore KEOPS. We now present a 3.4 Å crystal structure of a dimeric Kae1–Pcc1 complex providing direct evidence that Pcc1 can bind and dimerize Kae1. Further biophysical analysis of a complete archaeal KEOPS complex reveals that Pcc1 facilitates KEOPS dimerization in vitro. Interestingly, while Pcc1-mediated dimerization of KEOPS is required to support the growth of yeast, it is dispensable for t6A biosynthesis by archaeal KEOPS in vitro, raising the question of how precisely Pcc1-mediated dimerization impacts cellular biology.
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Affiliation(s)
- Leo C K Wan
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Monica C Pillon
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Neroshan Thevakumaran
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Yulong Sun
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5S 1L7, Canada
| | - Avi Chakrabartty
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada Department of Medical Biophysics, University of Toronto, Toronto, ON M5S 1L7, Canada
| | - Alba Guarné
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Igor Kurinov
- Cornell University, Department of Chemistry and Chemical Biology, NE-CAT, Building 436E, Advanced Photon Source, 9700 S. Cass Avenue, Argonne, IL 60439, USA
| | - Daniel Durocher
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Frank Sicheri
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
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18
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Thiaville PC, Iwata-Reuyl D, de Crécy-Lagard V. Diversity of the biosynthesis pathway for threonylcarbamoyladenosine (t(6)A), a universal modification of tRNA. RNA Biol 2015; 11:1529-39. [PMID: 25629598 PMCID: PMC4615747 DOI: 10.4161/15476286.2014.992277] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The tRNA modification field has a rich literature covering biochemical analysis going back more than 40 years, but many of the corresponding genes were only identified in the last decade. In recent years, comparative genomic-driven analysis has allowed for the identification of the genes and subsequent characterization of the enzymes responsible for N6-threonylcarbamoyladenosine (t6A). This universal modification, located in the anticodon stem-loop at position 37 adjacent to the anticodon of tRNAs, is found in nearly all tRNAs that decode ANN codons. The t6A biosynthesis enzymes and synthesis pathways have now been identified, revealing both a core set of enzymes and kingdom-specific variations. This review focuses on the elucidation of the pathway, diversity of the synthesis genes, and proposes a new nomenclature for t6A synthesis enzymes.
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Affiliation(s)
- Patrick C Thiaville
- a Genetics and Genomics Graduate Program ; University of Florida ; Gainesville , FL USA
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19
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The Structure of Escherichia coli TcdA (Also Known As CsdL) Reveals a Novel Topology and Provides Insight into the tRNA Binding Surface Required for N(6)-Threonylcarbamoyladenosine Dehydratase Activity. J Mol Biol 2015; 427:3074-85. [PMID: 26101842 DOI: 10.1016/j.jmb.2015.06.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 06/01/2015] [Accepted: 06/15/2015] [Indexed: 11/22/2022]
Abstract
Escherichia coli TcdA (also known as CsdL) was previously shown to catalyze the ATP-dependent dehydration/cyclization of hypermodified tRNA N(6)-threonylcarbamoyladenosine into further cyclic N(6)-threonylcarbamoyladenosine. In this study, we report the X-ray crystal structures of E. coli TcdA with either AMP or ATP bound. The AMP/ATP-bound N-terminal sub-domain of TcdA resembles the ATP-binding Rossmann fold of E. coli ThiF and MoeB that are enzymes respectively taking part in the biosynthesis of thiamine and molybdopterin; however, the remaining C-terminal sub-domain of TcdA adopts a structure unrelated to any other known folds. In TcdA, the ATP-utilizing adenylation of tRNA N(6)-threonylcarbamoyladenosine and a subsequent thioester formation via an active cysteine, similar to the mechanisms in ThiF and MoeB, could take place for the dehydratase function. Analysis of the structure with sequence alignment suggests the disordered Cys234 of TcdA as the most likely catalytic residue. The structure further indicates that the C-terminal sub-domain can provide a binding interface for the tRNA substrate. Binding study using the surface mutants of TcdA and tRNA reveals that the positively charged regions of mainly the C-terminal sub-domain are important for the tRNA recognition.
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20
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Rojas-Benitez D, Thiaville PC, de Crécy-Lagard V, Glavic A. The Levels of a Universally Conserved tRNA Modification Regulate Cell Growth. J Biol Chem 2015; 290:18699-707. [PMID: 26063805 DOI: 10.1074/jbc.m115.665406] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Indexed: 01/05/2023] Open
Abstract
N(6)-Threonylcarbamoyl-adenosine (t(6)A) is a universal modification occurring at position 37 in nearly all tRNAs that decode A-starting codons, including the eukaryotic initiator tRNA (tRNAi (Met)). Yeast lacking central components of the t(6)A synthesis machinery, such as Tcs3p (Kae1p) or Tcs5p (Bud32p), show slow-growth phenotypes. In the present work, we show that loss of the Drosophila tcs3 homolog also leads to a severe reduction in size and demonstrate, for the first time in a non-microbe, that Tcs3 is required for t(6)A synthesis. In Drosophila and in mammals, tRNAi (Met) is a limiting factor for cell and animal growth. We report that the t(6)A-modified form of tRNAi (Met) is the actual limiting factor. We show that changing the proportion of t(6)A-modified tRNAi (Met), by expression of an un-modifiable tRNAi (Met) or changing the levels of Tcs3, regulate target of rapamycin (TOR) kinase activity and influences cell and animal growth in vivo. These findings reveal an unprecedented relationship between the translation machinery and TOR, where translation efficiency, limited by the availability of t(6)A-modified tRNA, determines growth potential in eukaryotic cells.
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Affiliation(s)
- Diego Rojas-Benitez
- From the Centro de Regulación del Genoma, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Santiago, Chile 7800024 and
| | - Patrick C Thiaville
- the Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida32611-0700
| | - Valérie de Crécy-Lagard
- the Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida32611-0700
| | - Alvaro Glavic
- From the Centro de Regulación del Genoma, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Santiago, Chile 7800024 and
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21
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The crystal structure and small-angle X-ray analysis of CsdL/TcdA reveal a new tRNA binding motif in the MoeB/E1 superfamily. PLoS One 2015; 10:e0118606. [PMID: 25897750 PMCID: PMC4405576 DOI: 10.1371/journal.pone.0118606] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 01/21/2015] [Indexed: 11/19/2022] Open
Abstract
Cyclic N6-threonylcarbamoyladenosine ('cyclic t6A', ct(6)A) is a non-thiolated hypermodification found in transfer RNAs (tRNAs) in bacteria, protists, fungi and plants. In bacteria and yeast cells ct(6)A has been shown to enhance translation fidelity and efficiency of ANN codons by improving the faithful discrimination of aminoacylated tRNAs by the ribosome. To further the understanding of ct(6)A biology we have determined the high-resolution crystal structures of CsdL/TcdA in complex with AMP and ATP, an E1-like activating enzyme from Escherichia coli, which catalyzes the ATP-dependent dehydration of t6A to form ct(6)A. CsdL/TcdA is a dimer whose structural integrity and dimer interface depend critically on strongly bound K+ and Na+ cations. By using biochemical assays and small-angle X-ray scattering we show that CsdL/TcdA can associate with tRNA with a 1:1 stoichiometry and with the proper position and orientation for the cyclization of t6A. Furthermore, we show by nuclear magnetic resonance that CsdL/TcdA engages in transient interactions with CsdA and CsdE, which, in the latter case, involve catalytically important residues. These short-lived interactions may underpin the precise channeling of sulfur atoms from cysteine to CsdL/TcdA as previously characterized. In summary, the combination of structural, biophysical and biochemical methods applied to CsdL/TcdA has afforded a more thorough understanding of how the structure of this E1-like enzyme has been fine tuned to accomplish ct(6)A synthesis on tRNAs while providing support for the notion that CsdA and CsdE are able to functionally interact with CsdL/TcdA.
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22
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Abstract
Transfer RNAs (tRNAs) are central players in the protein translation machinery and as such are prominent targets for a large number of natural and synthetic antibiotics. This review focuses on the role of tRNAs in bacterial antibiosis. We will discuss examples of antibiotics that target multiple stages in tRNA biology from tRNA biogenesis and modification, mature tRNAs, aminoacylation of tRNA as well as prevention of proper tRNA function by small molecules binding to the ribosome. Finally, the role of deacylated tRNAs in the bacterial “stringent response” mechanism that can lead to bacteria displaying antibiotic persistence phenotypes will be discussed.
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23
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Kim S, Kim KY, Park JK, Lee BI, Kim YG, Park S. Overproduction, crystallization and preliminary X-ray crystallographic analysis of Escherichia coli tRNA N6-threonylcarbamoyladenosine dehydratase. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2014; 70:1517-20. [PMID: 25372820 DOI: 10.1107/s2053230x14020883] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 09/17/2014] [Indexed: 11/10/2022]
Abstract
Escherichia coli tRNA N6-threonylcarbamoyladenosine dehydratase (TcdA), previously called CsdL or YgdL, was overproduced and purified from E. coli and crystallized using polyethylene glycol 3350 as a crystallizing agent. X-ray diffraction data were collected to 2.70 Å resolution under cryoconditions using synchrotron X-rays. The crystals belonged to space group P2₁, with unit-cell parameters a=65.4, b=96.8, c=83.3 Å, β=111.7°. According to the Matthews coefficient, the asymmetric unit may contain up to four subunits of the monomeric protein, with a crystal volume per protein mass (VM) of 2.12 Å3 Da(-1) and 42.1% solvent content.
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Affiliation(s)
- Sunmin Kim
- School of Systems Biomedical Science, Soongsil University, Seoul 156-743, Republic of Korea
| | - Keon Young Kim
- School of Systems Biomedical Science, Soongsil University, Seoul 156-743, Republic of Korea
| | - Jeong Kuk Park
- School of Systems Biomedical Science, Soongsil University, Seoul 156-743, Republic of Korea
| | - Byung Il Lee
- Biomolecular Function Research Branch, Division of Convergence Technology, Research Institute, National Cancer Center, Goyang, Gyeonggi 410-769, Republic of Korea
| | - Yun-Gon Kim
- Department of Chemical Engineering, Soongsil University, Seoul 156-743, Republic of Korea
| | - SangYoun Park
- School of Systems Biomedical Science, Soongsil University, Seoul 156-743, Republic of Korea
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24
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Matuszewski M, Sochacka E. Stability studies on the newly discovered cyclic form of tRNA N6-threonylcarbamoyladenosine (ct6A). Bioorg Med Chem Lett 2014; 24:2703-6. [DOI: 10.1016/j.bmcl.2014.04.048] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 04/10/2014] [Accepted: 04/11/2014] [Indexed: 11/16/2022]
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25
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A cyclic form of N6-threonylcarbamoyladenosine as a widely distributed tRNA hypermodification. Nat Chem Biol 2012; 9:105-11. [PMID: 23242255 DOI: 10.1038/nchembio.1137] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 11/01/2012] [Indexed: 11/09/2022]
Abstract
N(6)-threonylcarbamoyladenosine (t(6)A) is a universally conserved, essential modified nucleoside found in transfer RNAs (tRNAs) responsible for ANN codons in all three domains of life. t(6)A has a crucial role in maintaining decoding accuracy during protein synthesis. The presence of t(6)A in cellular tRNAs has been well documented for more than four decades. However, under conditions optimized for nucleoside preparation, we detected little t(6)A in tRNAs from Escherichia coli. Instead, we identified a new modified base named 'cyclic t(6)A' (ct(6)A), which is a cyclized active ester with an oxazolone ring. An E1-like enzyme, CsdL (renamed as TcdA), which catalyzes ATP-dependent dehydration of t(6)A to form ct(6)A, was also identified. Two yeast homologs of tcdA, YHR003C (TCD1) and YKL027W (TCD2), were required for ct(6)A formation and respiratory cell growth. ct(6)A was involved in promoting decoding efficiency. Structural modeling suggests that ct(6)A recognizes the first adenine base of ANN codon at the ribosomal A site.
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26
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Lauhon CT. Mechanism of N6-threonylcarbamoyladenonsine (t(6)A) biosynthesis: isolation and characterization of the intermediate threonylcarbamoyl-AMP. Biochemistry 2012; 51:8950-63. [PMID: 23072323 DOI: 10.1021/bi301233d] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Genetic and biochemical studies have recently implicated four proteins required in bacteria for the biosynthesis of the universal tRNA modified base N6-threonylcarbamoyl adenosine (t(6)A). In this work, t(6)A biosynthesis in Bacillus subtilis has been reconstituted in vitro and found to indeed require the four proteins YwlC (TsaC), YdiB (TsaE), YdiC (TsaB) and YdiE (TsaD). YwlC was found to catalyze the conversion of L-threonine, bicarbonate/CO(2) and ATP to give the intermediate L-threonylcarbamoyl-AMP (TC-AMP) and pyrophosphate as products. TC-AMP was isolated by HPLC and characterized by mass spectrometry and (1)H NMR. NMR analysis showed that TC-AMP decomposes to give AMP and a nearly equimolar mixture of L-threonine and 5-methyl-2-oxazolidinone-4-carboxylate as final products. Under physiological conditions (pH 7.5, 37 °C, 2 mM MgCl(2)), the half-life of TC-AMP was measured to be 3.5 min. Both YwlC (in the presence of pyrophosphatase) and its Escherichia coli homologue YrdC catalyze the formation of TC-AMP while producing only a small molar fraction of AMP. This suggests that CO(2) and not an activated form of bicarbonate is the true substrate for these enzymes. In the presence of pyrophosphate, both enzymes catalyze clean conversion of TC-AMP back to ATP. Purified TC-AMP is efficiently processed to t(6)A by the YdiBCE proteins in the presence of tRNA substrates. This reaction is ATP independent in vitro, despite the known ATPase activity of YdiB. The estimated rate of conversion of TC-AMP by YdiBCE to t(6)A is somewhat lower than the initial rate from L-threonine, bicarbonate and ATP, which together with the stability data, is consistent with previous studies that suggest channeling of this intermediate.
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Affiliation(s)
- Charles T Lauhon
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison, Wisconsin 53705, United States.
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27
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Deutsch C, El Yacoubi B, de Crécy-Lagard V, Iwata-Reuyl D. Biosynthesis of threonylcarbamoyl adenosine (t6A), a universal tRNA nucleoside. J Biol Chem 2012; 287:13666-73. [PMID: 22378793 DOI: 10.1074/jbc.m112.344028] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The anticodon stem-loop (ASL) of transfer RNAs (tRNAs) drives decoding by interacting directly with the mRNA through codon/anticodon pairing. Chemically complex nucleoside modifications found in the ASL at positions 34 or 37 are known to be required for accurate decoding. Although over 100 distinct modifications have been structurally characterized in tRNAs, only a few are universally conserved, among them threonylcarbamoyl adenosine (t(6)A), found at position 37 in the anticodon loop of a subset of tRNA. Structural studies predict an important role for t(6)A in translational fidelity, and in vivo work supports this prediction. Although pioneering work in the 1970s identified the fundamental substrates for t(6)A biosynthesis, the enzymes responsible for its biosynthesis have remained an enigma. We report here the discovery that in bacteria four proteins (YgjD, YrdC, YjeE, and YeaZ) are both necessary and sufficient for t(6)A biosynthesis in vitro. Notably, YrdC and YgjD are members of universally conserved families that were ranked among the top 10 proteins of unknown function in need of functional characterization, while YeaZ and YjeE are specific to bacteria. This latter observation, coupled with the essentiality of all four proteins in bacteria, establishes this pathway as a compelling new target for antimicrobial development.
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Affiliation(s)
- Christopher Deutsch
- Department of Chemistry, Portland State University, Portland, Oregon 97207, USA
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28
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Giessing AMB, Kirpekar F. Mass spectrometry in the biology of RNA and its modifications. J Proteomics 2012; 75:3434-49. [PMID: 22348820 DOI: 10.1016/j.jprot.2012.01.032] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Revised: 01/20/2012] [Accepted: 01/26/2012] [Indexed: 01/31/2023]
Abstract
Many powerful analytical techniques for investigation of nucleic acids exist in the average modern molecular biology lab. The current review will focus on questions in RNA biology that have been answered by the use of mass spectrometry, which means that new biological information is the purpose and outcome of most of the studies we refer to. The review begins with a brief account of the subject "MS in the biology of RNA" and an overview of the prevalent RNA modifications identified to date. Fundamental considerations about mass spectrometric analysis of RNA are presented with the aim of detailing the analytical possibilities and challenges relating to the unique chemical nature of nucleic acids. The main biological topics covered are RNA modifications and the enzymes that perform the modifications. Modifications of RNA are essential in biology, and it is a field where mass spectrometry clearly adds knowledge of biological importance compared to traditional methods used in nucleic acid research. The biological applications are divided into analyses exclusively performed at the building block (mainly nucleoside) level and investigations involving mass spectrometry at the oligonucleotide level. We conclude the review discussing aspects of RNA identification and quantifications, which are upcoming fields for MS in RNA research. This article is part of a Special Section entitled: Understanding genome regulation and genetic diversity by mass spectrometry.
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Affiliation(s)
- Anders M B Giessing
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
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29
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Kuratani M, Kasai T, Akasaka R, Higashijima K, Terada T, Kigawa T, Shinkai A, Bessho Y, Yokoyama S. Crystal structure of Sulfolobus tokodaii Sua5 complexed with L-threonine and AMPPNP. Proteins 2011; 79:2065-75. [PMID: 21538543 DOI: 10.1002/prot.23026] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2010] [Revised: 01/31/2011] [Accepted: 02/25/2011] [Indexed: 11/09/2022]
Abstract
The hypermodified nucleoside N(6)-threonylcarbamoyladenosine resides at position 37 of tRNA molecules bearing U at position 36 and maintains translational fidelity in the three kingdoms of life. The N(6)-threonylcarbamoyl moiety is composed of L-threonine and bicarbonate, and its synthesis was genetically shown to require YrdC/Sua5. YrdC/Sua5 binds to tRNA and ATP. In this study, we analyzed the L-threonine-binding mode of Sua5 from the archaeon Sulfolobus tokodaii. Isothermal titration calorimetry measurements revealed that S. tokodaii Sua5 binds L-threonine more strongly than L-serine and glycine. The Kd values of Sua5 for L-threonine and L-serine are 9.3 μM and 2.6 mM, respectively. We determined the crystal structure of S. tokodaii Sua5, complexed with AMPPNP and L-threonine, at 1.8 Å resolution. The L-threonine is bound next to AMPPNP in the same pocket of the N-terminal domain. Thr118 and two water molecules form hydrogen bonds with AMPPNP in a unique manner for adenine-specific recognition. The carboxyl group and the side-chain hydroxyl and methyl groups of L-threonine are buried deep in the pocket, whereas the amino group faces AMPPNP. The L-threonine is located in a suitable position to react together with ATP for the synthesis of N(6)-threonylcarbamoyladenosine.
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Affiliation(s)
- Mitsuo Kuratani
- RIKEN Systems and Structural Biology Center, Yokohama 230-0045, Japan
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Mehler AH, Chakraburtty K. Some questions about the structure and activity of aminoacyl-tRNA synthetases. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2006; 35:443-501. [PMID: 4950472 DOI: 10.1002/9780470122808.ch8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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31
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Bajji AC, Davis DR. Synthesis of the tRNA(Lys,3) anticodon stem-loop domain containing the hypermodified ms2t6A nucleoside. J Org Chem 2002; 67:5352-8. [PMID: 12126427 DOI: 10.1021/jo025826t] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The synthesis of a protected form of the hypermodified nucleoside, N-[(9-beta-D-ribofuranosyl-2-methylthiopurin-6-yl)carbamoyl]threonine, (ms2t6A) is reported. The hypermodified nucleoside was subsequently elaborated to the protected nucleoside phosphophoramidite using a protecting group strategy compatible with standard RNA oligonucleotide chemistry. The phosphoramidite reagent was then used to synthesize the 17-nucleotide RNA hairpin having the sequence of the anticodon stem-loop (ASL) domain of human tRNA(Lys,3), the primer for HIV-1 reverse transcriptase. Introduction of the modification at position 37 of the tRNA ASL modestly decreases the thermodynamic stability of the RNA hairpin as has been seen previously for the prokaryotic t6A nucleoside lacking the 2-methylthio substituent. 2D NOESY NMR spectra of the ms2t6A containing tRNA ASL indicate that the threonyl side chain adopts a conformation similar to that seen in the solution structure of the analogous t6A containing E. coli tRNA(Lys), despite the presence of the bulky methylthio group. This synthetic approach allows for site-specific incorporation of the hypermodified nucleoside and should facilitate future studies directed at understanding the roles of nucleoside modification in modulating the stability and specificity of biologically important RNA-RNA interactions. Our synthesis of the ms2t6A containing RNAs demonstrates that this methodology is suitable for obtaining quantities of RNA required for structural studies of the HIV primer tRNA.
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Affiliation(s)
- Ashok C Bajji
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
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Abstract
The RNA modification database provides a comprehensive listing of post-transcriptionally modified nucleosides from RNA and is maintained as an updated version of the initial printed report. Information provided includes: type(s) of RNA in which found and phylogenetic distribution; common chemical names and symbols; Chemical Abstracts registry numbers and index names; chemical structures; initial literature citations for structural characterization or occurrence and chemical synthesis. The data are available through the World Wide Web, anonymous ftp or from the authors in printed form.
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Affiliation(s)
- P F Crain
- Department of Medicinal Chemistry, University of Utah, Salt Lake City 84112, USA
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Abstract
A comprehensive listing is made of posttranscriptionally modified nucleosides from RNA reported in the literature through mid-1994. Included are chemical structures, common names, symbols, Chemical Abstracts registry numbers (for ribonucleoside and corresponding base), Chemical Abstracts Index Name, phylogenetic sources, and initial literature citations for structural characterization or occurrence, and for chemical synthesis. The listing is categorized by type of RNA: tRNA, rRNA, mRNA, snRNA, and other RNAs. A total of 93 different modified nucleosides have been reported in RNA, with the largest number and greatest structural diversity in tRNA, 79; and 28 in rRNA, 12 in mRNA, 11 in snRNA and 3 in other small RNAs.
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Affiliation(s)
- P A Limbach
- Department of Medicinal Chemistry, University of Utah, Salt Lake City 84112
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Reddy DM, Crain PF, Edmonds CG, Gupta R, Hashizume T, Stetter KO, Widdel F, McCloskey JA. Structure determination of two new amino acid-containing derivatives of adenosine from tRNA of thermophilic bacteria and archaea. Nucleic Acids Res 1992; 20:5607-15. [PMID: 1280806 PMCID: PMC334393 DOI: 10.1093/nar/20.21.5607] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Two new nucleosides have been identified in unfractionated transfer RNA of two thermophilic bacteria, Thermodesulfobacterium commune, and Thermotoga maritima, six hyperthermophilic archaea, including Pyrobaculum islandicum, Pyrococcus furiosus and Thermococcus sp. and two mesophilic archaea, Methanococcus vannielii and Methanolobus tindarius. Structures were determined primarily by mass spectrometry, as 3-hydroxy-N-[[(9-beta-D-ribofuranosyl-9H-purin-6- yl)amino]carbonyl]norvaline, (hn6A), structure 1, and 3-hydroxy-N-[[(9-beta-D-ribofuranosyl-9H-2-methylthiopurin-6- yl)amino]carbonyl]norvaline (ms2hn6A), 2. The amino acid side chain was characterized as 3-hydroxynorvaline (3) by gas chromatography-mass spectrometry of the trimethylsilyl derivative after cleavage from 1 and 2 by alkaline hydrolysis. Evidence for the amino acid-purine carbamoyl linkage was obtained from the collision-induced dissociation mass spectrum of trimethylsilylated 1, and the total structure was confirmed by chemical synthesis of 1.
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Affiliation(s)
- D M Reddy
- Department of Medicinal Chemistry, University of Utah, Salt Lake City 84112
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35
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Tewari R. Conformational preferences of modified nucleic acid bases N6-methyl-N6-(N-threonylcarbonyl) adenine and 2-methylthio-N6-(N-threonylcarbonyl) adenine by the quantum chemical PCILO calculations. J Biomol Struct Dyn 1990; 8:675-86. [PMID: 2129236 DOI: 10.1080/07391102.1990.10507835] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Conformational preferences of the hypermodified nucleic acid bases N6-methyl-N6-(N-threonylcarbonyl) Adenine, m6tc6 Ade, and 2-methylthio-N6-(N-threonylcarbonyl) Adenine, mS2 tc6 Ade, have been studied theoretically using the quantum chemical PCILO (Perturbative Configuration Interaction using Localized Orbitals) method. The multidimensional conformational space has been searched using selected grid points formed by combining the various torsion angles which take the favoured values obtained from energy variation with respect to each torsion angle individually. In m6 tc6 Ade and mS 2tc6 Ade alike the threonylcarbonyl substituent preferably orients away (distal) from the imidazole moiety of the adenine ring. And as in the simpler N6-(N-threonylcarbonyl) Adenine, tc6 Ade, the atoms in the ureido group as well as the amino acid carbon atoms C(12) and C(13) remain coplanar with the purine base. As in tc6 Ade, this conformation is stabilized by the intramolecular hydrogen bond between N(11)H of the amino acid and N(1) of the adenine base. The N6-methyl protons, in m6 tc6 Ade, take trans-staggered orientation with respect to the C(6)-N(6) bond. The preferred orientation of the 2-methylthio group is cis to the C(2)-N(3) bond in mS 2tc6 Ade. This is in marked contrast to the modified nucleic acid base 2-methylthio-N6-(delta 2-isopentenyl) Adenine, mS 2i6 Ade, where the 2-methylthio group orients trans to the C(2)-N(3) bond, causing a change in the preferred orientation of the isopentenyl component on methylthiolation. The present results thus indicate that unlike in the isopentenyl adenine the role of further chemical substitutions in threonylcarbonyl adenine may be indirect and less pronounced.
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Affiliation(s)
- R Tewari
- Physical Chemistry Division, National Chemical Laboratory, Pune, India
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36
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Ajitkumar P, Cherayil JD. Thionucleosides in transfer ribonucleic acid: diversity, structure, biosynthesis, and function. Microbiol Rev 1988; 52:103-13. [PMID: 3280963 PMCID: PMC372707 DOI: 10.1128/mr.52.1.103-113.1988] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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37
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Reddy RP, Schweizer MP, Chheda GB. Interaction of the tRNA-derived unusual nucleoside, t6A, with Mn(II) and Mg(II). FEBS Lett 1979; 106:63-6. [PMID: 499504 DOI: 10.1016/0014-5793(79)80695-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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38
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Schweizer MP, Hamill WD. Carbon-13 NMR studies on the interaction of manganese ion with the tRNA derived modified nucleoside, t6Aa. Biochem Biophys Res Commun 1978; 85:1367-72. [PMID: 743304 DOI: 10.1016/0006-291x(78)91154-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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39
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Watts MT, Tinoco I. Role of hypermodified bases in transfer RNA. Solution properties of dinucleoside monophosphates. Biochemistry 1978; 17:2455-63. [PMID: 678525 DOI: 10.1021/bi00605a033] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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40
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KASAI H, MURAO K, NISHIMURA S, LIEHR JG, CRAIN PF, McCLOSKEY JA. Structure Determination of a Modified Nucleoside Isolated from Escherichia coli Transfer Ribonucleic Acid. N-[N-[(9-beta-d-Ribofuranosylpurin-6-yl)carbamoyl]threonyl]2-amido-2-hydroxymethylpropane-1,3-diol. ACTA ACUST UNITED AC 1976. [DOI: 10.1111/j.1432-1033.1976.tb10928.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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41
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Miller JP, Hussain Z, Schweizer MP. The involvement of the anticodon adjacent modified nucleoside N-(9-(BETA-D-ribofuranosyl) purine-6-ylcarbamoyl)-threonine in the biological function of E. coli tRNAile. Nucleic Acids Res 1976; 3:1185-201. [PMID: 781621 PMCID: PMC342979 DOI: 10.1093/nar/3.5.1185] [Citation(s) in RCA: 37] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
tRNAile was isolated from E. coli Cp 79 (leu-, arg-, thr-, his-, thiamin-, RCrel) which had been grown on a sub-optimal concentration of thr and was found to contain an average of 50% less N-[9-(beta-D-ribofuranosyl)- purin-6-ylcarbamoyl]threonine, t6Ado, than tRNAile from cells grown on an optimum concentration of thr and containing a normal complement of t6Ado. The two tRNA's were identical in their ability to be aminoacylated, to accept the 3'-terminal dinucleotide, and to form an ile-tRNAile-Tu-GTP complex. In contrast, the t6Ado-deficient-tRNA was significantly less efficient in binding to ribosomes compared to the normal tRNA. This difference was seen in the binding of deacylated tRNA and in the nonenzymatic and enzymatic binding of ile-tRNA, all in response to poly AUC. The t6Ado-deficient ile-tRNA demonstrated no binding at Mg2+ concentrations less than or equal to 10 mM, while the normal ile-tRNA bound at low Mg2+ concentrations. Tetracycline had the same effect on the normal as on the t6Ado-deficient ile-tRNA binding. As a control, the binding of phe-tRNA (which does not contain t6Ado) from normal and thr-starved cells in response to poly U was identical. It was concluded that t6Ado is required for proper codon-anticodon interaction.
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42
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Fournier MJ, Peterkofsky A. Formation of chromatographically unique species of transfer ribonucleic acid during amino acid starvation of relaxed-control Escherichia coli. J Bacteriol 1975; 122:538-48. [PMID: 1092655 PMCID: PMC246089 DOI: 10.1128/jb.122.2.538-548.1975] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Examination of the transfer ribonucleic acid (tRNA) produced by starving, relaxed-control (rel minus) strains of Escherichia coli for required amino acids revealed the occurrence of a number of chromatographically unique subspecies. Leucine starvation results in the formation of new isoacceptor species of leucine-, histidine-, arginine-, valine-, and phenylalanine-specific tRNA and quantitative changes in the column profiles of serine, glycine, and isoleucine tRNA. Evidence that the unique tRNA species are synthesized de novo during amino acid starvation comes from the findings that the major unique leucine isoacceptor species is not formed in stringent control cells or in rel minus cells starved for uracil or treated with rifampin. Furthermore, heat treatment of the unique leucine tRNA does not alter its chromatographic behavior, indicating that the species is not an aggregate or nuclease-damaged form of a normal isoacceptor tRNA. The methyl acceptor activities of tRNA from leucine-starved and nonstarved rel+ or rel minus cells were found to be essentially the same. This result and the finding that the chromatographic behavior of the unique leucine-specific tRNA was not altered after treatment with tRNA methylase suggests that gross methyl deficiency is probably not the biochemical basis for the occurrence of the unique species.
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43
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Parthasarathy R, Ohrt JM, Chheda GB. Conformation and possible role of hypermodified nucleosides adjacent to 3'-end of anticodon in tRNA: N-(purin-6-ylcarbamoyl)-L-threonine riboside. Biochem Biophys Res Commun 1974; 60:211-8. [PMID: 4423161 DOI: 10.1016/0006-291x(74)90193-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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44
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Thedford R, Straus DB. Some helical interactions of poly(N6-(delta 2-isopentenyl)adenylic acid). Biochemistry 1974; 13:535-42. [PMID: 4810065 DOI: 10.1021/bi00700a021] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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45
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Neelon FA, Birch BM, Lebovitz HE. Preparative solvent partition chromatography of butyrylated cyclic AMP analogues. Anal Biochem 1973; 56:74-83. [PMID: 4358020 DOI: 10.1016/0003-2697(73)90171-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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46
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Hong CI, Chheda GB, Murphy GP, Mittelman A. Metabolism of N-(purin-6-ylcarbamoyl)-L-threonine riboside in rat and man. Biochem Pharmacol 1973; 22:1927-36. [PMID: 4722460 DOI: 10.1016/0006-2952(73)90053-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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47
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The Nucleotide Sequences and Coding Properties of the Major and Minor Lysine Transfer Ribonucleic Acids from the Haploid Yeast Saccharomyces cerevisiae αS288C. J Biol Chem 1973. [DOI: 10.1016/s0021-9258(19)43792-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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48
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Serebryanyi AM, Mnatsakanyan RM. A study of the molecular mechanism of the mutagenic action of N-nitroso-N-alkylurea. Carbamoylation of nucleosides by N-nitroso-N-alkylureas. FEBS Lett 1972; 28:191-194. [PMID: 11946855 DOI: 10.1016/0014-5793(72)80709-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- A M. Serebryanyi
- Institute of Chemical Physics, USSR Academy of Sciences, V-334, Moscow, USSR
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49
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Miller JP, Schweizer MP. Determination of N-(9-( -D-ribofuranosyl)purin-6-ylcarbamoly)threonine at the picomole level in transfer-RNA. Anal Biochem 1972; 50:327-36. [PMID: 4345787 DOI: 10.1016/0003-2697(72)90041-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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50
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Simsek M, RajBhandary UL. The primary structure of yeast initiator transfer ribonucleic acid. Biochem Biophys Res Commun 1972; 49:508-15. [PMID: 4344891 DOI: 10.1016/0006-291x(72)90440-8] [Citation(s) in RCA: 117] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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