1
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Salem MG, Alqahtani AM, Mali SN, Alshwyeh HA, Jawarkar RD, Altamimi AS, Alshawwa SZ, Al-Olayan E, Saied EM, Youssef MF. Synthesis and antiproliferative evaluation of novel 3,5,8-trisubstituted coumarins against breast cancer. Future Med Chem 2024; 16:1053-1073. [PMID: 38708686 PMCID: PMC11216633 DOI: 10.4155/fmc-2023-0375] [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: 12/11/2023] [Accepted: 02/13/2024] [Indexed: 05/07/2024] Open
Abstract
Aim: This study focused on designing and synthesizing novel derivatives of 3,5,8-trisubstituted coumarin. Results: The synthesized compounds, particularly compound 5, exhibited significant cytotoxic effects on MCF-7 cells, surpassing staurosporine, and reduced toxicity toward MCF-10A cells, highlighting potential pharmacological advantages. Further, compound 5 altered the cell cycle and significantly increased apoptosis in MCF-7 cells, involving both early (41.7-fold) and late stages (33-fold), while moderately affecting necrotic signaling. The antitumor activity was linked to a notable reduction (4.78-fold) in topoisomerase IIβ expression. Molecular modeling indicated compound 5's strong affinity for EGFR, human EGF2 and topoisomerase II proteins. Conclusion: These findings highlight compound 5 as a multifaceted antitumor agent for breast cancer.
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Affiliation(s)
- Manar G Salem
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Suez Canal University, Ismailia, 41522, Egypt
| | - Alaa M Alqahtani
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Umm Al-Qura University, Makkah, 21955, Saudi Arabia
| | - Suraj N Mali
- School of Pharmacy, DY Patil Deemed to be University Sector 7, Nerul, Navi Mumbai, 400706, India
| | - Hussah Abdullah Alshwyeh
- Department of Biology, College of Science, Imam Abdulrahman Bin Faisal University, Dammam, 31441, Saudi Arabia
- Basic & Applied Scientific Research Centre, Imam Abdulrahman Bin Faisal University, PO Box 1982, Dammam, 31441, Saudi Arabia
| | - Rahul D Jawarkar
- Department of Medicinal Chemistry & Drug Discovery, Dr. Rajendra Gode Institute of Pharmacy, University Mardi Road, Amravati, 444603, India
| | - Abdulmalik S Altamimi
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, PO Box 173, Alkharj, 11942, Saudi Arabia
| | - Samar Z Alshawwa
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah bint Abdulrahman University, PO Box 84428, Riyadh, 11671, Saudi Arabia
| | - Ebtesam Al-Olayan
- Department of Zoology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Essa M Saied
- Chemistry Department (Biochemistry Division), Faculty of Science, Suez Canal University, Ismailia, 41522, Egypt
- Institute for Chemistry, Humboldt Universität zu Berlin, Brook-Taylor-Str. 2, Berlin, 12489, Germany
| | - Mohamed F Youssef
- Chemistry Department (Organic Chemistry Division), Faculty of Science, Suez Canal University, Ismailia, 41522, Egypt
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2
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Serrano IM, Hirose M, Valentine CC, Roesner S, Schmidt E, Pratt G, Williams L, Salk J, Ibrahim S, Sudmant PH. Mitochondrial haplotype and mito-nuclear matching drive somatic mutation and selection throughout ageing. Nat Ecol Evol 2024; 8:1021-1034. [PMID: 38361161 PMCID: PMC11090800 DOI: 10.1038/s41559-024-02338-3] [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: 03/08/2023] [Accepted: 01/22/2024] [Indexed: 02/17/2024]
Abstract
Mitochondrial genomes co-evolve with the nuclear genome over evolutionary timescales and are shaped by selection in the female germline. Here we investigate how mismatching between nuclear and mitochondrial ancestry impacts the somatic evolution of the mitochondrial genome in different tissues throughout ageing. We used ultrasensitive duplex sequencing to profile ~2.5 million mitochondrial genomes across five mitochondrial haplotypes and three tissues in young and aged mice, cataloguing ~1.2 million mitochondrial somatic and ultralow-frequency inherited mutations, of which 81,097 are unique. We identify haplotype-specific mutational patterns and several mutational hotspots, including at the light strand origin of replication, which consistently exhibits the highest mutation frequency. We show that rodents exhibit a distinct mitochondrial somatic mutational spectrum compared with primates with a surfeit of reactive oxygen species-associated G > T/C > A mutations, and that somatic mutations in protein-coding genes exhibit signatures of negative selection. Lastly, we identify an extensive enrichment in somatic reversion mutations that 're-align' mito-nuclear ancestry within an organism's lifespan. Together, our findings demonstrate that mitochondrial genomes are a dynamically evolving subcellular population shaped by somatic mutation and selection throughout organismal lifetimes.
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Affiliation(s)
- Isabel M Serrano
- Center for Computational Biology, University of California, Berkeley, CA, USA
| | - Misa Hirose
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | | | | | | | | | | | - Jesse Salk
- TwinStrand Biosciences, Seattle, WA, USA
| | - Saleh Ibrahim
- College of Medicine, Khalifa University, Abu Dhabi, UAE
| | - Peter H Sudmant
- Center for Computational Biology, University of California, Berkeley, CA, USA.
- Department of Integrative Biology, University of California, Berkeley, CA, USA.
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3
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Andac CA, Hornemann U, Noyanalpan N, Stringfellow TC. Synthesis, NMR kinetics and dynamic structure of a 17-mer heptaloop RNA hairpin carrying a 3- N-methyluridine nucleotide residue in the loop region. J Biomol Struct Dyn 2024; 42:3659-3681. [PMID: 37278223 DOI: 10.1080/07391102.2023.2214231] [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: 11/21/2022] [Accepted: 05/10/2023] [Indexed: 06/07/2023]
Abstract
A 17-mer RNA hairpin (5'GGGAGUXAGCGGCUCCC3') carrying 3-N-methyluridine (m3U) at position X (m3U7-RNA), designed to represent the anticodon stem-loop (ACSL) region of tRNAs to study an open loop state (O-state), was synthesized, purified by HPLC, and characterized by MALDI-ToF_MS and NMR methods. 1H-NMR data revealed primary (P-state in 56.1%), secondary (S-state in 43.9%) and tertiary (∼5-6%) ACSL conformations. Exchange rate constant (kex) for interconversion between P and S states is 112 sec-1 (<Δω ∼454 rad/sec), confirming a slow exchange regime between the two states. Forward (kPS) and backward (kSP) rate constants are 49.166 sec-1 and 62.792 sec-1, respectively, leading to a longer life-time (20.339 msec) for the P-state and a shorter life-time (15.926 msec) for the S-state. In accordance with conformational populations determined by 1H-NMR, dynamics of the P/S/tertiary states of m3U7-RNA and its wild-type counterpart (wt-RNA) were studied by three independent MD production simulations. Cluster analysis revealed that wt-RNA reflects the structural characteristics of the ACSL region of tRNAs. The P-state of m3U7-RNA was found to be structurally similar to wt-RNA but lacks an intraloop H-bond between m3U7 and C10 (U33 and nt36 in tRNAs). In the S-state of m3U7-RNA, m3U7 flips out of the loop region. O-state loop conformations of m3U7-RNA were also clustered (4.8%), wherein the loop nucleotides m3U7.A8.G9.C10.G11 stack one after another. We propose that the O-state of m3U7-RNA is the most suitable conformation that makes the loop accessible for complementary nucleotides and for non-enzymatic primordial replication of small circular RNAs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Cenk A Andac
- Department of Medical Pharmacology, School of Medicine, Yeditepe University, Istanbul, Turkiye
| | - Ulfert Hornemann
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
| | - Ningur Noyanalpan
- Department of Medicinal Chemistry, School of Pharmacy, Gazi University, Ankara, Turkiye
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4
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Kompatscher M, Bartosik K, Erharter K, Plangger R, Juen F, Kreutz C, Micura R, Westhof E, Erlacher M. Contribution of tRNA sequence and modifications to the decoding preferences of E. coli and M. mycoides tRNAGlyUCC for synonymous glycine codons. Nucleic Acids Res 2024; 52:1374-1386. [PMID: 38050960 PMCID: PMC10853795 DOI: 10.1093/nar/gkad1136] [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: 09/13/2023] [Revised: 11/06/2023] [Accepted: 11/10/2023] [Indexed: 12/07/2023] Open
Abstract
tRNA superwobbling, used by certain bacteria and organelles, is an intriguing decoding concept in which a single tRNA isoacceptor is used to decode all synonymous codons of a four-fold degenerate codon box. While Escherichia coli relies on three tRNAGly isoacceptors to decode the four glycine codons (GGN), Mycoplasma mycoides requires only a single tRNAGly. Both organisms express tRNAGly with the anticodon UCC, which are remarkably similar in sequence but different in their decoding ability. By systematically introducing mutations and altering the number and type of tRNA modifications using chemically synthesized tRNAs, we elucidated the contribution of individual nucleotides and chemical groups to decoding by the E. coli and M. mycoides tRNAGly. The tRNA sequence was identified as the key factor for superwobbling, revealing the T-arm sequence as a novel pivotal element. In addition, the presence of tRNA modifications, although not essential for providing superwobbling, was shown to delicately fine-tune and balance the decoding of synonymous codons. This emphasizes that the tRNA sequence and its modifications together form an intricate system of high complexity that is indispensable for accurate and efficient decoding.
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Affiliation(s)
- Maria Kompatscher
- Institute of Genomics and RNomics, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Karolina Bartosik
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Kevin Erharter
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Raphael Plangger
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Fabian Sebastian Juen
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Christoph Kreutz
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Eric Westhof
- Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, Architecture et Réactivité de l’ARN, CNRS UPR 9002, 2, allée Konrad Roentgen, F-67084 Strasbourg, France
| | - Matthias D Erlacher
- Institute of Genomics and RNomics, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
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5
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Sabalette KB, Makarova L, Marcia M. G·U base pairing motifs in long non-coding RNAs. Biochimie 2023; 214:123-140. [PMID: 37353139 DOI: 10.1016/j.biochi.2023.06.003] [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: 04/27/2023] [Revised: 06/08/2023] [Accepted: 06/09/2023] [Indexed: 06/25/2023]
Abstract
Long non-coding RNAs (lncRNAs) are recently-discovered transcripts involved in gene expression regulation and associated with diseases. Despite the unprecedented molecular complexity of these transcripts, recent studies of the secondary and tertiary structure of lncRNAs are starting to reveal the principles of lncRNA structural organization, with important functional implications. It therefore starts to be possible to analyze lncRNA structures systematically. Here, using a set of prototypical and medically-relevant lncRNAs of known secondary structure, we specifically catalogue the distribution and structural environment of one of the first-identified and most frequently occurring non-canonical Watson-Crick interactions, the G·U base pair. We compare the properties of G·U base pairs in our set of lncRNAs to those of the G·U base pairs in other well-characterized transcripts, like rRNAs, tRNAs, ribozymes, and riboswitches. Furthermore, we discuss how G·U base pairs in these targets participate in establishing interactions with proteins or miRNAs, and how they enable lncRNA tertiary folding by forming intramolecular or metal-ion interactions. Finally, by identifying highly-G·U-enriched regions of yet unknown function in our target lncRNAs, we provide a new rationale for future experimental investigation of these motifs, which will help obtain a more comprehensive understanding of lncRNA functions and molecular mechanisms in the future.
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Affiliation(s)
- Karina Belen Sabalette
- European Molecular Biology Laboratory (EMBL) Grenoble, 71 Avenue des Martyrs, Grenoble, 38042, France
| | - Liubov Makarova
- European Molecular Biology Laboratory (EMBL) Grenoble, 71 Avenue des Martyrs, Grenoble, 38042, France
| | - Marco Marcia
- European Molecular Biology Laboratory (EMBL) Grenoble, 71 Avenue des Martyrs, Grenoble, 38042, France.
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6
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Serrano IM, Hirose M, Valentine CC, Roesner S, Schmidt E, Pratt G, Williams L, Salk J, Ibrahim S, Sudmant PH. Mitochondrial haplotype and mito-nuclear matching drive somatic mutation and selection throughout aging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.06.531392. [PMID: 36945529 PMCID: PMC10028854 DOI: 10.1101/2023.03.06.531392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Mitochondrial genomes co-evolve with the nuclear genome over evolutionary timescales and are shaped by selection in the female germline. Here, we investigate how mismatching between nuclear and mitochondrial ancestry impacts the somatic evolution of the mt-genome in different tissues throughout aging. We used ultra-sensitive Duplex Sequencing to profile ~2.5 million mt-genomes across five mitochondrial haplotypes and three tissues in young and aged mice, cataloging ~1.2 million mitochondrial somatic and ultra low frequency inherited mutations, of which 81,097 are unique. We identify haplotype-specific mutational patterns and several mutational hotspots, including at the Light Strand Origin of Replication, which consistently exhibits the highest mutation frequency. We show that rodents exhibit a distinct mitochondrial somatic mutational spectrum compared to primates with a surfeit of reactive oxygen species-associated G>T/C>A mutations, and that somatic mutations in protein coding genes exhibit signatures of negative selection. Lastly, we identify an extensive enrichment in somatic reversion mutations that "re-align" mito-nuclear ancestry within an organism's lifespan. Together, our findings demonstrate that mitochondrial genomes are a dynamically evolving subcellular population shaped by somatic mutation and selection throughout organismal lifetimes.
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Affiliation(s)
- Isabel M Serrano
- Center for Computational Biology, University of California, Berkeley
| | - Misa Hirose
- Lübeck Institute of Experimental Dermatology, University of Lübeck
| | | | | | | | | | | | | | - Saleh Ibrahim
- Department of Integrative Biology, University of California, Berkeley
| | - Peter H Sudmant
- Center for Computational Biology, University of California, Berkeley
- Department of Integrative Biology, University of California, Berkeley
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7
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Ali Z, Kaur S, Kukhta T, Abu-Saleh AAAA, Jhunjhunwala A, Mitra A, Trant JF, Sharma P. Structural Mapping of the Base Stacks Containing Post-transcriptionally Modified Bases in RNA. J Phys Chem B 2023. [PMID: 37369074 DOI: 10.1021/acs.jpcb.3c02268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Post-transcriptionally modified bases play vital roles in many biochemical processes involving RNA. Analysis of the non-covalent interactions associated with these bases in RNA is crucial for providing a more complete understanding of the RNA structure and function; however, the characterization of these interactions remains understudied. To address this limitation, we present a comprehensive analysis of base stacks involving all crystallographic occurrences of the most biologically relevant modified bases in a large dataset of high-resolution RNA crystal structures. This is accompanied by a geometrical classification of the stacking contacts using our established tools. Coupled with quantum chemical calculations and an analysis of the specific structural context of these stacks, this provides a map of the stacking conformations available to modified bases in RNA. Overall, our analysis is expected to facilitate structural research on altered RNA bases.
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Affiliation(s)
- Zakir Ali
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India
| | - Sarabjeet Kaur
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India
- Surface Chemistry and Catalysis: Characterisation and Application Team (COK-KAT), Leuven (Arenberg) Celestijnenlaan 200f─Box 2461, 3001 Leuven, Belgium
| | - Teagan Kukhta
- Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, Ontario N9B 3P4, Canada
| | - Abd Al-Aziz A Abu-Saleh
- Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, Ontario N9B 3P4, Canada
- Binary Star Research Services, LaSalle, Ontario N9J 3X8, Canada
| | - Ayush Jhunjhunwala
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad, Telangana 500032, India
| | - Abhijit Mitra
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad, Telangana 500032, India
| | - John F Trant
- Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, Ontario N9B 3P4, Canada
- Binary Star Research Services, LaSalle, Ontario N9J 3X8, Canada
| | - Purshotam Sharma
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India
- Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, Ontario N9B 3P4, Canada
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8
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Vögele J, Duchardt-Ferner E, Kruse H, Zhang Z, Sponer J, Krepl M, Wöhnert J. Structural and dynamic effects of pseudouridine modifications on noncanonical interactions in RNA. RNA (NEW YORK, N.Y.) 2023; 29:790-807. [PMID: 36868785 PMCID: PMC10187676 DOI: 10.1261/rna.079506.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 02/10/2023] [Indexed: 05/18/2023]
Abstract
Pseudouridine is the most frequently naturally occurring RNA modification, found in all classes of biologically functional RNAs. Compared to uridine, pseudouridine contains an additional hydrogen bond donor group and is therefore widely regarded as a structure stabilizing modification. However, the effects of pseudouridine modifications on the structure and dynamics of RNAs have so far only been investigated in a limited number of different structural contexts. Here, we introduced pseudouridine modifications into the U-turn motif and the adjacent U:U closing base pair of the neomycin-sensing riboswitch (NSR)-an extensively characterized model system for RNA structure, ligand binding, and dynamics. We show that the effects of replacing specific uridines with pseudouridines on RNA dynamics crucially depend on the exact location of the replacement site and can range from destabilizing to locally or even globally stabilizing. By using a combination of NMR spectroscopy, MD simulations and QM calculations, we rationalize the observed effects on a structural and dynamical level. Our results will help to better understand and predict the consequences of pseudouridine modifications on the structure and function of biologically important RNAs.
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Affiliation(s)
- Jennifer Vögele
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Elke Duchardt-Ferner
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Holger Kruse
- Institute of Biophysics of the Czech Academy of Sciences, 612 65 Brno, Czech Republic
| | - Zhengyue Zhang
- Institute of Biophysics of the Czech Academy of Sciences, 612 65 Brno, Czech Republic
- CEITEC-Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Jiri Sponer
- Institute of Biophysics of the Czech Academy of Sciences, 612 65 Brno, Czech Republic
| | - Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences, 612 65 Brno, Czech Republic
| | - Jens Wöhnert
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, 60438 Frankfurt, Germany
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9
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General Strategies for RNA X-ray Crystallography. Molecules 2023; 28:molecules28052111. [PMID: 36903357 PMCID: PMC10004510 DOI: 10.3390/molecules28052111] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 02/22/2023] [Accepted: 02/22/2023] [Indexed: 02/27/2023] Open
Abstract
An extremely small proportion of the X-ray crystal structures deposited in the Protein Data Bank are of RNA or RNA-protein complexes. This is due to three main obstacles to the successful determination of RNA structure: (1) low yields of pure, properly folded RNA; (2) difficulty creating crystal contacts due to low sequence diversity; and (3) limited methods for phasing. Various approaches have been developed to address these obstacles, such as native RNA purification, engineered crystallization modules, and incorporation of proteins to assist in phasing. In this review, we will discuss these strategies and provide examples of how they are used in practice.
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10
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Dolce LG, Zimmer AA, Tengo L, Weis F, Rubio MAT, Alfonzo JD, Kowalinski E. Structural basis for sequence-independent substrate selection by eukaryotic wobble base tRNA deaminase ADAT2/3. Nat Commun 2022; 13:6737. [PMID: 36347890 PMCID: PMC9643335 DOI: 10.1038/s41467-022-34441-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 10/26/2022] [Indexed: 11/09/2022] Open
Abstract
The essential deamination of adenosine A34 to inosine at the wobble base is the individual tRNA modification with the greatest effects on mRNA decoding, empowering a single tRNA to translate three different codons. To date, many aspects of how eukaryotic deaminases specifically select their multiple substrates remain unclear. Here, using cryo-EM, we present the structure of a eukaryotic ADAT2/3 deaminase bound to a full-length tRNA, revealing that the enzyme distorts the anticodon loop, but in contrast to the bacterial enzymes, selects its substrate via sequence-independent contacts of eukaryote-acquired flexible or intrinsically unfolded motifs distal from the conserved catalytic core. A gating mechanism for substrate entry to the active site is identified. Our multi-step tRNA recognition model yields insights into how RNA editing by A34 deamination evolved, shaped the genetic code, and directly impacts the eukaryotic proteome.
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Affiliation(s)
- Luciano G Dolce
- EMBL Grenoble, 71 Avenue des Martyrs, 38042, Grenoble, France
| | - Aubree A Zimmer
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Laura Tengo
- EMBL Grenoble, 71 Avenue des Martyrs, 38042, Grenoble, France
| | - Félix Weis
- EMBL Heidelberg, Structural and Computational Biology Unit, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Mary Anne T Rubio
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Juan D Alfonzo
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Eva Kowalinski
- EMBL Grenoble, 71 Avenue des Martyrs, 38042, Grenoble, France.
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11
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Harp JM, Lybrand TP, Pallan PS, Coates L, Sullivan B, Egli M. Cryo neutron crystallography demonstrates influence of RNA 2'-OH orientation on conformation, sugar pucker and water structure. Nucleic Acids Res 2022; 50:7721-7738. [PMID: 35819202 PMCID: PMC9303348 DOI: 10.1093/nar/gkac577] [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] [Received: 03/21/2022] [Revised: 06/15/2022] [Accepted: 06/21/2022] [Indexed: 11/14/2022] Open
Abstract
The ribose 2′-hydroxyl is the key chemical difference between RNA and DNA and primary source of their divergent structural and functional characteristics. Macromolecular X-ray diffraction experiments typically do not reveal the positions of hydrogen atoms. Thus, standard crystallography cannot determine 2′-OH orientation (H2′-C2′-O2′-HO2′ torsion angle) and its potential roles in sculpting the RNA backbone and the expansive fold space. Here, we report the first neutron crystal structure of an RNA, the Escherichia coli rRNA Sarcin-Ricin Loop (SRL). 2′-OD orientations were established for all 27 residues and revealed O-D bonds pointing toward backbone (O3′, 13 observations), nucleobase (11) or sugar (3). Most riboses in the SRL stem region show a 2′-OD backbone-orientation. GAGA-tetraloop riboses display a 2′-OD base-orientation. An atypical C2′-endo sugar pucker is strictly correlated with a 2′-OD sugar-orientation. Neutrons reveal the strong preference of the 2′-OH to donate in H-bonds and that 2′-OH orientation affects both backbone geometry and ribose pucker. We discuss 2′-OH and water molecule orientations in the SRL neutron structure and compare with results from a solution phase 10 μs MD simulation. We demonstrate that joint cryo-neutron/X-ray crystallography offers an all-in-one approach to determine the complete structural properties of RNA, i.e. geometry, conformation, protonation state and hydration structure.
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Affiliation(s)
- Joel M Harp
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA.,Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Terry P Lybrand
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA.,Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Pradeep S Pallan
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA.,Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Leighton Coates
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Brendan Sullivan
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Martin Egli
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA.,Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
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12
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Finet O, Yague-Sanz C, Marchand F, Hermand D. The Dihydrouridine landscape from tRNA to mRNA: a perspective on synthesis, structural impact and function. RNA Biol 2022; 19:735-750. [PMID: 35638108 PMCID: PMC9176250 DOI: 10.1080/15476286.2022.2078094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The universal dihydrouridine (D) epitranscriptomic mark results from a reduction of uridine by the Dus family of NADPH-dependent reductases and is typically found within the eponym D-loop of tRNAs. Despite its apparent simplicity, D is structurally unique, with the potential to deeply affect the RNA backbone and many, if not all, RNA-connected processes. The first landscape of its occupancy within the tRNAome was reported 20 years ago. Its potential biological significance was highlighted by observations ranging from a strong bias in its ecological distribution to the predictive nature of Dus enzymes overexpression for worse cancer patient outcomes. The exquisite specificity of the Dus enzymes revealed by a structure-function analyses and accumulating clues that the D distribution may expand beyond tRNAs recently led to the development of new high-resolution mapping methods, including Rho-seq that established the presence of D within mRNAs and led to the demonstration of its critical physiological relevance.
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Affiliation(s)
- Olivier Finet
- URPHYM-GEMO, The University of Namur, Namur, Belgium
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13
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Trachman RJ, Passalacqua LFM, Ferré-D'Amaré AR. The bacterial yjdF riboswitch regulates translation through its tRNA-like fold. J Biol Chem 2022; 298:101934. [PMID: 35427649 PMCID: PMC9142559 DOI: 10.1016/j.jbc.2022.101934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/08/2022] [Accepted: 04/09/2022] [Indexed: 10/27/2022] Open
Abstract
Unlike most riboswitches, which have one cognate effector, the bacterial yjdF riboswitch binds to diverse azaaromatic compounds, only a subset of which cause it to activate translation. We examined the yjdF aptamer domain by small-angle X-ray scattering, and found that in the presence of activating ligands, the RNA adopts an overall shape similar to that of tRNA. Sequence analyses suggested that the yjdF aptamer is a homolog of tRNALys, and that two of the conserved loops of the riboswitch are equivalent to the D- and T-loops of tRNA, associating to form an elbow-like tertiary interaction. Chemical probing indicated that this association is promoted by activating ligands such as chelerythrine and harmine. In its native mRNA context, activator ligands stabilize the tRNA-like fold of the yjdF aptamer, outcompeting the attenuated state in which its T-loop base-pairs to the Shine-Dalgarno element of the mRNA. Moreover, we demonstrate that the liganded aptamer itself activates translation, as authentic tRNAs, when grafted into mRNA, can potently activate translation. Taken together, our data demonstrate the ability of tRNA to function as a small-molecule responsive cis regulatory element.
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Affiliation(s)
- Robert J Trachman
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, 50 South Drive MSC 8012, Bethesda, MD 20892-8012, USA.
| | - Luiz F M Passalacqua
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, 50 South Drive MSC 8012, Bethesda, MD 20892-8012, USA
| | - Adrian R Ferré-D'Amaré
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, 50 South Drive MSC 8012, Bethesda, MD 20892-8012, USA
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14
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Westhof E, Thornlow B, Chan PP, Lowe TM. Eukaryotic tRNA sequences present conserved and amino acid-specific structural signatures. Nucleic Acids Res 2022; 50:4100-4112. [PMID: 35380696 PMCID: PMC9023262 DOI: 10.1093/nar/gkac222] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 03/16/2022] [Accepted: 03/22/2022] [Indexed: 11/18/2022] Open
Abstract
Metazoan organisms have many tRNA genes responsible for decoding amino acids. The set of all tRNA genes can be grouped in sets of common amino acids and isoacceptor tRNAs that are aminoacylated by corresponding aminoacyl-tRNA synthetases. Analysis of tRNA alignments shows that, despite the high number of tRNA genes, specific tRNA sequence motifs are highly conserved across multicellular eukaryotes. The conservation often extends throughout the isoacceptors and isodecoders with, in some cases, two sets of conserved isodecoders. This study is focused on non-Watson–Crick base pairs in the helical stems, especially GoU pairs. Each of the four helical stems may contain one or more conserved GoU pairs. Some are amino acid specific and could represent identity elements for the cognate aminoacyl tRNA synthetases. Other GoU pairs are found in more than a single amino acid and could be critical for native folding of the tRNAs. Interestingly, some GoU pairs are anticodon-specific, and others are found in phylogenetically-specific clades. Although the distribution of conservation likely reflects a balance between accommodating isotype-specific functions as well as those shared by all tRNAs essential for ribosomal translation, such conservations may indicate the existence of specialized tRNAs for specific translation targets, cellular conditions, or alternative functions.
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Affiliation(s)
- Eric Westhof
- Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, Architecture et Réactivité de l'ARN, CNRS UPR 9002, 2, allée Konrad Roentgen, F-67084 Strasbourg, France
| | - Bryan Thornlow
- Department of Biomolecular Engineering, Baskin School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.,UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Patricia P Chan
- Department of Biomolecular Engineering, Baskin School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.,UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Todd M Lowe
- Department of Biomolecular Engineering, Baskin School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.,UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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15
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Ye S, Lehmann J. Genetic code degeneracy is established by the decoding center of the ribosome. Nucleic Acids Res 2022; 50:4113-4126. [PMID: 35325219 PMCID: PMC9023292 DOI: 10.1093/nar/gkac171] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 02/10/2022] [Accepted: 03/23/2022] [Indexed: 11/21/2022] Open
Abstract
The degeneracy of the genetic code confers a wide array of properties to coding sequences. Yet, its origin is still unclear. A structural analysis has shown that the stability of the Watson–Crick base pair at the second position of the anticodon–codon interaction is a critical parameter controlling the extent of non-specific pairings accepted at the third position by the ribosome, a flexibility at the root of degeneracy. Based on recent cryo-EM analyses, the present work shows that residue A1493 of the decoding center provides a significant contribution to the stability of this base pair, revealing that the ribosome is directly involved in the establishment of degeneracy. Building on existing evolutionary models, we show the evidence that the early appearance of A1493 and A1492 established the basis of degeneracy when an elementary kinetic scheme of translation was prevailing. Logical considerations on the expansion of this kinetic scheme indicate that the acquisition of the peptidyl transferase center was the next major evolutionary step, while the induced-fit mechanism, that enables a sharp selection of the tRNAs, necessarily arose later when G530 was acquired by the decoding center.
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Affiliation(s)
- Shixin Ye
- INSERM U1195 unit, University of Paris-Saclay, 94276 Le Kremlin Bicêtre, France
| | - Jean Lehmann
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University of Paris-Saclay, 91198 Gif-sur-Yvette, France
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16
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Skeparnias I, Zhang J. Cooperativity and Interdependency between RNA Structure and RNA-RNA Interactions. Noncoding RNA 2021; 7:ncrna7040081. [PMID: 34940761 PMCID: PMC8704770 DOI: 10.3390/ncrna7040081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 11/16/2022] Open
Abstract
Complex RNA–RNA interactions are increasingly known to play key roles in numerous biological processes from gene expression control to ribonucleoprotein granule formation. By contrast, the nature of these interactions and characteristics of their interfaces, especially those that involve partially or wholly structured RNAs, remain elusive. Herein, we discuss different modalities of RNA–RNA interactions with an emphasis on those that depend on secondary, tertiary, or quaternary structure. We dissect recently structurally elucidated RNA–RNA complexes including RNA triplexes, riboswitches, ribozymes, and reverse transcription complexes. These analyses highlight a reciprocal relationship that intimately links RNA structure formation with RNA–RNA interactions. The interactions not only shape and sculpt RNA structures but also are enabled and modulated by the structures they create. Understanding this two-way relationship between RNA structure and interactions provides mechanistic insights into the expanding repertoire of noncoding RNA functions, and may inform the design of novel therapeutics that target RNA structures or interactions.
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17
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Jeong H, Kim J. Unique anticodon loop conformation with the flipped-out wobble nucleotide in the crystal structure of unbound tRNA Val. RNA (NEW YORK, N.Y.) 2021; 27:1330-1338. [PMID: 34315814 PMCID: PMC8522699 DOI: 10.1261/rna.078863.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 07/24/2021] [Indexed: 06/13/2023]
Abstract
During protein synthesis on ribosome, tRNA recognizes its cognate codon of mRNA through base-pairing with the anticodon. The 5'-end nucleotide of the anticodon is capable of wobble base-pairing, offering a molecular basis for codon degeneracy. The wobble nucleotide is often targeted for post-transcriptional modification, which affects the specificity and fidelity of the decoding process. Flipping-out of a wobble nucleotide in the anticodon loop has been proposed to be necessary for modifying enzymes to access the target nucleotide, which has been captured in selective structures of protein-bound complexes. Meanwhile, all other structures of free or ribosome-bound tRNA display anticodon bases arranged in stacked conformation. We report the X-ray crystal structure of unbound tRNAVal1 to a 2.04 Å resolution showing two different conformational states of wobble uridine in the anticodon loop, one stacked on the neighboring base and the other swiveled out toward solvent. In addition, the structure reveals a rare magnesium ion coordination to the nitrogen atom of a nucleobase, which has been sampled very rarely among known structures of nucleic acids.
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MESH Headings
- Anticodon/chemistry
- Anticodon/genetics
- Anticodon/metabolism
- Base Pairing
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Metals/metabolism
- Models, Molecular
- Nucleic Acid Conformation
- Protein Biosynthesis
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Transfer, Val/chemistry
- RNA, Transfer, Val/genetics
- RNA, Transfer, Val/metabolism
- Ribosomes/genetics
- Ribosomes/metabolism
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Affiliation(s)
- Hyeonju Jeong
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Jungwook Kim
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
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18
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Blersch KF, Burchert JP, August SC, Welp L, Neumann P, Köster S, Urlaub H, Ficner R. Structural model of the M7G46 Methyltransferase TrmB in complex with tRNA. RNA Biol 2021; 18:2466-2479. [PMID: 34006170 DOI: 10.1080/15476286.2021.1925477] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
TrmB belongs to the class I S-adenosylmethionine (SAM)-dependent methyltransferases (MTases) and introduces a methyl group to guanine at position 7 (m7G) in tRNA. In tRNAs m7G is most frequently found at position 46 in the variable loop and forms a tertiary base pair with C13 and U22, introducing a positive charge at G46. The TrmB/Trm8 enzyme family is structurally diverse, as TrmB proteins exist in a monomeric, homodimeric, and heterodimeric form. So far, the exact enzymatic mechanism, as well as the tRNA-TrmB crystal structure is not known. Here we present the first crystal structures of B. subtilis TrmB in complex with SAM and SAH. The crystal structures of TrmB apo and in complex with SAM and SAH have been determined by X-ray crystallography to 1.9 Å (apo), 2.5 Å (SAM), and 3.1 Å (SAH). The obtained crystal structures revealed Tyr193 to be important during SAM binding and MTase activity. Applying fluorescence polarization, the dissociation constant Kd of TrmB and tRNAPhe was determined to be 0.12 µM ± 0.002 µM. Luminescence-based methyltransferase activity assays revealed cooperative effects during TrmB catalysis with half-of-the-site reactivity at physiological SAM concentrations. Structural data retrieved from small-angle x-ray scattering (SAXS), mass-spectrometry of cross-linked complexes, and molecular docking experiments led to the determination of the TrmB-tRNAPhe complex structure.
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Affiliation(s)
- Katharina F Blersch
- Department of Molecular Structural Biology, Institute of Microbiology and Genetics, GZMB, Georg August University Göttingen, Göttingen, Germany
| | - Jan-Philipp Burchert
- Institute for X-Ray Physics, Georg August University Göttingen, Göttingen, Germany
| | | | - Luisa Welp
- Bioanalytical Mass Spectrometry Research Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Piotr Neumann
- Department of Molecular Structural Biology, Institute of Microbiology and Genetics, GZMB, Georg August University Göttingen, Göttingen, Germany
| | - Sarah Köster
- Institute for X-Ray Physics, Georg August University Göttingen, Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Research Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Bioanalytics Group, Institute for Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Ralf Ficner
- Department of Molecular Structural Biology, Institute of Microbiology and Genetics, GZMB, Georg August University Göttingen, Göttingen, Germany
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19
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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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20
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Post-Transcriptional Modifications of Conserved Nucleotides in the T-Loop of tRNA: A Tale of Functional Convergent Evolution. Genes (Basel) 2021; 12:genes12020140. [PMID: 33499018 PMCID: PMC7912444 DOI: 10.3390/genes12020140] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/18/2021] [Accepted: 01/20/2021] [Indexed: 12/30/2022] Open
Abstract
The high conservation of nucleotides of the T-loop, including their chemical identity, are hallmarks of tRNAs from organisms belonging to the three Domains of Life. These structural characteristics allow the T-loop to adopt a peculiar intraloop conformation able to interact specifically with other conserved residues of the D-loop, which ultimately folds the mature tRNA in a unique functional canonical L-shaped architecture. Paradoxically, despite the high conservation of modified nucleotides in the T-loop, enzymes catalyzing their formation depend mostly on the considered organism, attesting for an independent but convergent evolution of the post-transcriptional modification processes. The driving force behind this is the preservation of a native conformation of the tRNA elbow that underlies the various interactions of tRNA molecules with different cellular components.
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21
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Liu Y, Chen Y. Mitochondrial tRNA Mutations Associated With Essential Hypertension: From Molecular Genetics to Function. Front Cell Dev Biol 2021; 8:634137. [PMID: 33585472 PMCID: PMC7874112 DOI: 10.3389/fcell.2020.634137] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 12/28/2020] [Indexed: 11/13/2022] Open
Abstract
Essential hypertension (EH) is one of the most common cardiovascular diseases worldwide, entailing a high level of morbidity. EH is a multifactorial disease influenced by both genetic and environmental factors, including mitochondrial DNA (mtDNA) genotype. Previous studies identified mtDNA mutations that are associated with maternally inherited hypertension, including tRNAIle m.4263A>G, m.4291T>C, m.4295A>G, tRNAMet m.4435A>G, tRNAAla m.5655A>G, and tRNAMet/tRNAGln m.4401A>G, et al. These mtDNA mutations alter tRNA structure, thereby leading to metabolic disorders. Metabolic defects associated with mitochondrial tRNAs affect protein synthesis, cause oxidative phosphorylation defects, reduced ATP synthesis, and increase production of reactive oxygen species. In this review we discuss known mutations of tRNA genes encoded by mtDNA and the potential mechanisms by which these mutations may contribute to hypertension.
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Affiliation(s)
- Yuqi Liu
- Cardiac Department, Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, China.,Department of Cardiology & National Clinical Research Center of Geriatrics Disease, Chinese PLA General Hospital, Beijing, China.,Beijing Key Laboratory of Chronic Heart Failure Precision Medicine, Chinese PLA General Hospital, Beijing, China.,National Key Laboratory of Kidney Diseases, Chinese PLA General Hospital, Beijing, China
| | - Yundai Chen
- Cardiac Department, Chinese PLA General Hospital, Beijing, China
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22
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Huh D, Passarelli MC, Gao J, Dusmatova SN, Goin C, Fish L, Pinzaru AM, Molina H, Ren Z, McMillan EA, Asgharian H, Goodarzi H, Tavazoie SF. A stress-induced tyrosine-tRNA depletion response mediates codon-based translational repression and growth suppression. EMBO J 2021; 40:e106696. [PMID: 33346941 PMCID: PMC7809793 DOI: 10.15252/embj.2020106696] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 12/16/2022] Open
Abstract
Eukaryotic transfer RNAs can become selectively fragmented upon various stresses, generating tRNA-derived small RNA fragments. Such fragmentation has been reported to impact a small fraction of the tRNA pool and thus presumed to not directly impact translation. We report that oxidative stress can rapidly generate tyrosine-tRNAGUA fragments in human cells-causing significant depletion of the precursor tRNA. Tyrosine-tRNAGUA depletion impaired translation of growth and metabolic genes enriched in cognate tyrosine codons. Depletion of tyrosine tRNAGUA or its translationally regulated targets USP3 and SCD repressed proliferation-revealing a dedicated tRNA-regulated growth-suppressive pathway for oxidative stress response. Tyrosine fragments are generated in a DIS3L2 exoribonuclease-dependent manner and inhibit hnRNPA1-mediated transcript destabilization. Moreover, tyrosine fragmentation is conserved in C. elegans. Thus, tRNA fragmentation can coordinately generate trans-acting small RNAs and functionally deplete a tRNA. Our findings reveal the existence of an underlying adaptive codon-based regulatory response inherent to the genetic code.
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Affiliation(s)
- Doowon Huh
- Laboratory of Systems Cancer BiologyThe Rockefeller UniversityNew YorkNYUSA
| | - Maria C Passarelli
- Laboratory of Systems Cancer BiologyThe Rockefeller UniversityNew YorkNYUSA
| | - Jenny Gao
- Laboratory of Systems Cancer BiologyThe Rockefeller UniversityNew YorkNYUSA
| | | | - Clara Goin
- Laboratory of Systems Cancer BiologyThe Rockefeller UniversityNew YorkNYUSA
| | - Lisa Fish
- Department of Biochemistry & BiophysicsUniversity of California, San FranciscoSan FranciscoCAUSA
| | | | - Henrik Molina
- Proteome Resource CenterThe Rockefeller UniversityNew YorkNYUSA
| | - Zhiji Ren
- Laboratory of Systems Cancer BiologyThe Rockefeller UniversityNew YorkNYUSA
| | | | - Hosseinali Asgharian
- Department of Biochemistry & BiophysicsUniversity of California, San FranciscoSan FranciscoCAUSA
| | - Hani Goodarzi
- Department of Biochemistry & BiophysicsUniversity of California, San FranciscoSan FranciscoCAUSA
| | - Sohail F Tavazoie
- Laboratory of Systems Cancer BiologyThe Rockefeller UniversityNew YorkNYUSA
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23
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Pallan PS, Lybrand TP, Schlegel MK, Harp JM, Jahns H, Manoharan M, Egli M. Incorporating a Thiophosphate Modification into a Common RNA Tetraloop Motif Causes an Unanticipated Stability Boost. Biochemistry 2020; 59:4627-4637. [PMID: 33275419 DOI: 10.1021/acs.biochem.0c00685] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
GNRA (N = A, C, G, or U; R = A or G) tetraloops are common RNA secondary structural motifs and feature a phosphate stacked atop a nucleobase. The rRNA sarcin/ricin loop (SRL) is capped by GApGA, and the phosphate p stacks on G. We recently found that regiospecific incorporation of a single dithiophosphate (PS2) but not a monothiophosphate (PSO) instead of phosphate in the backbone of RNA aptamers dramatically increases the binding affinity for their targets. In the RNA:thrombin complex, the key contribution to the 1000-fold tighter binding stems from an edge-on contact between PS2 and a phenylalanine ring. Here we investigated the consequences of replacing the SRL phosphate engaged in a face-on interaction with guanine with either PS2 or PSO for stability. We found that PS2···G and Rp-PSO···G contacts stabilize modified SRLs compared to the parent loop to unexpected levels: up to 6.3 °C in melting temperature Tm and -4.7 kcal/mol in ΔΔG°. Crystal structures demonstrate that the vertical distance to guanine for the closest sulfur is just 0.05 Å longer on average compared to that of oxygen despite the larger van der Waals radius of the former (1.80 Å for S vs 1.52 Å for O). The higher stability is enthalpy-based, and the negative charge as assessed by a neutral methylphosphonate modification plays only a minor role. Quantum mechanical/molecular mechanical calculations are supportive of favorable dispersion attraction interactions by sulfur making the dominant contribution. A stacking interaction between phosphate and guanine (SRL) or uracil (U-turn) is also found in newly classified RNA tetraloop families besides GNRA.
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Affiliation(s)
| | | | - Mark K Schlegel
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, Massachusetts 02142, United States
| | | | - Hartmut Jahns
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Muthiah Manoharan
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, Massachusetts 02142, United States
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24
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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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25
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Westhof E, Liang S, Tong X, Ding X, Zheng L, Dai F. Unusual tertiary pairs in eukaryotic tRNA Ala. RNA (NEW YORK, N.Y.) 2020; 26:1519-1529. [PMID: 32737189 PMCID: PMC7566577 DOI: 10.1261/rna.076299.120] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 07/28/2020] [Indexed: 05/08/2023]
Abstract
tRNA molecules have well-defined sequence conservations that reflect the conserved tertiary pairs maintaining their architecture and functions during the translation processes. An analysis of aligned tRNA sequences present in the GtRNAdb database (the Lowe Laboratory, University of California, Santa Cruz) led to surprising conservations on some cytosolic tRNAs specific for alanine compared to other tRNA species, including tRNAs specific for glycine. First, besides the well-known G3oU70 base pair in the amino acid stem, there is the frequent occurrence of a second wobble pair at G30oU40, a pair generally observed as a Watson-Crick pair throughout phylogeny. Second, the tertiary pair R15/Y48 occurs as a purine-purine R15/A48 pair. Finally, the conserved T54/A58 pair maintaining the fold of the T-loop is observed as a purine-purine A54/A58 pair. The R15/A48 and A54/A58 pairs always occur together. The G30oU40 pair occurs alone or together with these other two pairs. The pairing variations are observed to a variable extent depending on phylogeny. Among eukaryotes, insects display all variations simultaneously, whereas mammals present either the G30oU40 pair or both R15/A48 and A54/A58. tRNAs with the anticodon 34A(I)GC36 are the most prone to display all those pair variations in mammals and insects. tRNAs with anticodon Y34GC36 have preferentially G30oU40 only. These unusual pairs are not observed in bacterial, nor archaeal, tRNAs, probably because of the avoidance of A34-containing anticodons in four-codon boxes. Among eukaryotes, these unusual pairing features were not observed in fungi and nematodes. These unusual structural features may affect, besides aminoacylation, transcription rates (e.g., 54/58) or ribosomal translocation (30/40).
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Affiliation(s)
- Eric Westhof
- State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing 400715, China
- Architecture et Réactivité de l'ARN, Institut e Biologie Moléculaire et Cellulaire, UPR9002 CNRS, Université de Strasbourg, Strasbourg 67084, France
| | - Shubo Liang
- State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing 400715, China
| | - Xiaoling Tong
- State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing 400715, China
| | - Xin Ding
- State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing 400715, China
| | - Lu Zheng
- State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing 400715, China
| | - Fangyin Dai
- State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing 400715, China
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26
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A Structural Basis for Restricted Codon Recognition Mediated by 2-thiocytidine in tRNA Containing a Wobble Position Inosine. J Mol Biol 2020; 432:913-929. [PMID: 31945376 DOI: 10.1016/j.jmb.2019.12.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 11/25/2019] [Accepted: 12/05/2019] [Indexed: 11/20/2022]
Abstract
Three of six arginine codons (CGU, CGC, and CGA) are decoded by two Escherichia coli tRNAArg isoacceptors. The anticodon stem and loop (ASL) domains of tRNAArg1 and tRNAArg2 both contain inosine and 2-methyladenosine modifications at positions 34 (I34) and 37 (m2A37). tRNAArg1 is also modified from cytidine to 2-thiocytidine at position 32 (s2C32). The s2C32 modification is known to negate wobble codon recognition of the rare CGA codon by an unknown mechanism, while still allowing decoding of CGU and CGC. Substitution of s2C32 for C32 in the Saccharomyces cerevisiae tRNAIleIAU anticodon stem and loop domain (ASL) negates wobble decoding of its synonymous A-ending codon, suggesting that this function of s2C at position 32 is a generalizable property. X-ray crystal structures of variously modified ASLArg1ICG and ASLArg2ICG constructs bound to cognate and wobble codons on the ribosome revealed the disruption of a C32-A38 cross-loop interaction but failed to fully explain the means by which s2C32 restricts I34 wobbling. Computational studies revealed that the adoption of a spatially broad inosine-adenosine base pair at the wobble position of the codon cannot be maintained simultaneously with the canonical ASL U-turn motif. C32-A38 cross-loop interactions are required for stability of the anticodon/codon interaction in the ribosomal A-site.
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27
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A tRNA- and Anticodon-Centric View of the Evolution of Aminoacyl-tRNA Synthetases, tRNAomes, and the Genetic Code. Life (Basel) 2019; 9:life9020037. [PMID: 31060233 PMCID: PMC6616430 DOI: 10.3390/life9020037] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 04/24/2019] [Accepted: 05/01/2019] [Indexed: 11/25/2022] Open
Abstract
Pathways of standard genetic code evolution remain conserved and apparent, particularly upon analysis of aminoacyl-tRNA synthetase (aaRS) lineages. Despite having incompatible active site folds, class I and class II aaRS are homologs by sequence. Specifically, structural class IA aaRS enzymes derive from class IIA aaRS enzymes by in-frame extension of the protein N-terminus and by an alternate fold nucleated by the N-terminal extension. The divergence of aaRS enzymes in the class I and class II clades was analyzed using the Phyre2 protein fold recognition server. The class I aaRS radiated from the class IA enzymes, and the class II aaRS radiated from the class IIA enzymes. The radiations of aaRS enzymes bolster the coevolution theory for evolution of the amino acids, tRNAomes, the genetic code, and aaRS enzymes and support a tRNA anticodon-centric perspective. We posit that second- and third-position tRNA anticodon sequence preference (C>(U~G)>A) powerfully selected the sectoring pathway for the code. GlyRS-IIA appears to have been the primordial aaRS from which all aaRS enzymes evolved, and glycine appears to have been the primordial amino acid around which the genetic code evolved.
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28
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Westhof E, Yusupov M, Yusupova G. The multiple flavors of GoU pairs in RNA. J Mol Recognit 2019; 32:e2782. [PMID: 31033092 PMCID: PMC6617799 DOI: 10.1002/jmr.2782] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 03/02/2019] [Accepted: 03/14/2019] [Indexed: 11/10/2022]
Abstract
Wobble GU pairs (or GoU) occur frequently within double‐stranded RNA helices interspersed within the standard G═C and A─U Watson‐Crick pairs. However, other types of GoU pairs interacting on their Watson‐Crick edges have been observed. The structural and functional roles of such alternative GoU pairs are surprisingly diverse and reflect the various pairings G and U can form by exploiting all the subtleties of their electronic configurations. Here, the structural characteristics of the GoU pairs are updated following the recent crystallographic structures of functional ribosomal complexes and the development in our understanding of ribosomal translation.
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Affiliation(s)
- Eric Westhof
- Architecture et Réactivité de l'ARN, Institut de biologie moléculaire et cellulaire du CNRS, Université de Strasbourg, Strasbourg, France
| | - Marat Yusupov
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, INSERM, U964, CNRS, UMR7104, Université de Strasbourg, Illkirch, France
| | - Gulnara Yusupova
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, INSERM, U964, CNRS, UMR7104, Université de Strasbourg, Illkirch, France
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29
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The RNA degradosome promotes tRNA quality control through clearance of hypomodified tRNA. Proc Natl Acad Sci U S A 2019; 116:1394-1403. [PMID: 30622183 DOI: 10.1073/pnas.1814130116] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The factors and mechanisms that govern tRNA stability in bacteria are not well understood. Here, we investigated the influence of posttranscriptional modification of bacterial tRNAs (tRNA modification) on tRNA stability. We focused on ThiI-generated 4-thiouridine (s4U), a modification found in bacterial and archaeal tRNAs. Comprehensive quantification of Vibrio cholerae tRNAs revealed that the abundance of some tRNAs is decreased in a ΔthiI strain in a stationary phase-specific manner. Multiple mechanisms, including rapid degradation of a subset of hypomodified tRNAs, account for the reduced abundance of tRNAs in the absence of thiI Through transposon insertion sequencing, we identified additional tRNA modifications that promote tRNA stability and bacterial viability. Genetic analysis of suppressor mutants as well as biochemical analyses revealed that rapid degradation of hypomodified tRNA is mediated by the RNA degradosome. Elongation factor Tu seems to compete with the RNA degradosome, protecting aminoacyl tRNAs from decay. Together, our observations describe a previously unrecognized bacterial tRNA quality control system in which hypomodification sensitizes tRNAs to decay mediated by the RNA degradosome.
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30
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7-Methylguanosine Modifications in Transfer RNA (tRNA). Int J Mol Sci 2018; 19:ijms19124080. [PMID: 30562954 PMCID: PMC6320965 DOI: 10.3390/ijms19124080] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/05/2018] [Accepted: 12/13/2018] [Indexed: 01/15/2023] Open
Abstract
More than 90 different modified nucleosides have been identified in tRNA. Among the tRNA modifications, the 7-methylguanosine (m7G) modification is found widely in eubacteria, eukaryotes, and a few archaea. In most cases, the m7G modification occurs at position 46 in the variable region and is a product of tRNA (m7G46) methyltransferase. The m7G46 modification forms a tertiary base pair with C13-G22, and stabilizes the tRNA structure. A reaction mechanism for eubacterial tRNA m7G methyltransferase has been proposed based on the results of biochemical, bioinformatic, and structural studies. However, an experimentally determined mechanism of methyl-transfer remains to be ascertained. The physiological functions of m7G46 in tRNA have started to be determined over the past decade. For example, tRNA m7G46 or tRNA (m7G46) methyltransferase controls the amount of other tRNA modifications in thermophilic bacteria, contributes to the pathogenic infectivity, and is also associated with several diseases. In this review, information of tRNA m7G modifications and tRNA m7G methyltransferases is summarized and the differences in reaction mechanism between tRNA m7G methyltransferase and rRNA or mRNA m7G methylation enzyme are discussed.
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31
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Šponer J, Bussi G, Krepl M, Banáš P, Bottaro S, Cunha RA, Gil-Ley A, Pinamonti G, Poblete S, Jurečka P, Walter NG, Otyepka M. RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview. Chem Rev 2018; 118:4177-4338. [PMID: 29297679 PMCID: PMC5920944 DOI: 10.1021/acs.chemrev.7b00427] [Citation(s) in RCA: 336] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Indexed: 12/14/2022]
Abstract
With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics. Computer simulations, and in particular atomistic molecular dynamics (MD), allow structural dynamics of biomolecular systems to be investigated with unprecedented temporal and spatial resolution. We here provide a comprehensive overview of the fast-developing field of MD simulations of RNA molecules. We begin with an in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods. We also survey the closely related field of coarse-grained modeling of RNA systems. After dealing with the methodological aspects, we provide an exhaustive overview of the available RNA simulation literature, ranging from studies of the smallest RNA oligonucleotides to investigations of the entire ribosome. Our review encompasses tetranucleotides, tetraloops, a number of small RNA motifs, A-helix RNA, kissing-loop complexes, the TAR RNA element, the decoding center and other important regions of the ribosome, as well as assorted others systems. Extended sections are devoted to RNA-ion interactions, ribozymes, riboswitches, and protein/RNA complexes. Our overview is written for as broad of an audience as possible, aiming to provide a much-needed interdisciplinary bridge between computation and experiment, together with a perspective on the future of the field.
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Affiliation(s)
- Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences , Kralovopolska 135 , Brno 612 65 , Czech Republic
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences , Kralovopolska 135 , Brno 612 65 , Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Sandro Bottaro
- Structural Biology and NMR Laboratory, Department of Biology , University of Copenhagen , Copenhagen 2200 , Denmark
| | - Richard A Cunha
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Alejandro Gil-Ley
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Giovanni Pinamonti
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Simón Poblete
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Petr Jurečka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Nils G Walter
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
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32
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Branciamore S, Gogoshin G, Di Giulio M, Rodin AS. Intrinsic Properties of tRNA Molecules as Deciphered via Bayesian Network and Distribution Divergence Analysis. Life (Basel) 2018; 8:life8010005. [PMID: 29419741 PMCID: PMC5871937 DOI: 10.3390/life8010005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 01/22/2018] [Accepted: 01/23/2018] [Indexed: 12/27/2022] Open
Abstract
The identity/recognition of tRNAs, in the context of aminoacyl tRNA synthetases (and other molecules), is a complex phenomenon that has major implications ranging from the origins and evolution of translation machinery and genetic code to the evolution and speciation of tRNAs themselves to human mitochondrial diseases to artificial genetic code engineering. Deciphering it via laboratory experiments, however, is difficult and necessarily time- and resource-consuming. In this study, we propose a mathematically rigorous two-pronged in silico approach to identifying and classifying tRNA positions important for tRNA identity/recognition, rooted in machine learning and information-theoretic methodology. We apply Bayesian Network modeling to elucidate the structure of intra-tRNA-molecule relationships, and distribution divergence analysis to identify meaningful inter-molecule differences between various tRNA subclasses. We illustrate the complementary application of these two approaches using tRNA examples across the three domains of life, and identify and discuss important (informative) positions therein. In summary, we deliver to the tRNA research community a novel, comprehensive methodology for identifying the specific elements of interest in various tRNA molecules, which can be followed up by the corresponding experimental work and/or high-resolution position-specific statistical analyses.
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Affiliation(s)
- Sergio Branciamore
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, City of Hope, Duarte, 91010 CA, USA.
| | - Grigoriy Gogoshin
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, City of Hope, Duarte, 91010 CA, USA.
| | - Massimo Di Giulio
- Early Evolution of Life Laboratory, Institute of Biosciences and Bioresources, CNR, 80131 Naples, Italy.
| | - Andrei S Rodin
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, City of Hope, Duarte, 91010 CA, USA.
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33
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Abstract
We advocate for a tRNA- rather than an mRNA-centric model for evolution of the genetic code. The mechanism for evolution of cloverleaf tRNA provides a root sequence for radiation of tRNAs and suggests a simplified understanding of code evolution. To analyze code sectoring, rooted tRNAomes were compared for several archaeal and one bacterial species. Rooting of tRNAome trees reveals conserved structures, indicating how the code was shaped during evolution and suggesting a model for evolution of a LUCA tRNAome tree. We propose the polyglycine hypothesis that the initial product of the genetic code may have been short chain polyglycine to stabilize protocells. In order to describe how anticodons were allotted in evolution, the sectoring-degeneracy hypothesis is proposed. Based on sectoring, a simple stepwise model is developed, in which the code sectors from a 1→4→8→∼16 letter code. At initial stages of code evolution, we posit strong positive selection for wobble base ambiguity, supporting convergence to 4-codon sectors and ∼16 letters. In a later stage, ∼5–6 letters, including stops, were added through innovating at the anticodon wobble position. In archaea and bacteria, tRNA wobble adenine is negatively selected, shrinking the maximum size of the primordial genetic code to 48 anticodons. Because 64 codons are recognized in mRNA, tRNA-mRNA coevolution requires tRNA wobble position ambiguity leading to degeneracy of the code.
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Affiliation(s)
- Daewoo Pak
- a Center for Statistical Training and Consulting , Michigan State University , E. Lansing , MI 48824 , USA
| | - Nan Du
- b Computer Science and Engineering , Michigan State University , E. Lansing , MI 48824
| | | | - Yanni Sun
- b Computer Science and Engineering , Michigan State University , E. Lansing , MI 48824
| | - Zachary F Burton
- d Department of Biochemistry and Molecular Biology , Michigan State University , E. Lansing , MI 48824-1319
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34
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Sonawane KD, Kamble AS, Fandilolu PM. Preferences of AAA/AAG codon recognition by modified nucleosides, τm 5s 2U 34 and t 6A 37 present in tRNA Lys. J Biomol Struct Dyn 2017; 36:4182-4196. [PMID: 29243556 DOI: 10.1080/07391102.2017.1417911] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Deficiency of 5-taurinomethyl-2-thiouridine, τm5s2U at the 34th 'wobble' position in tRNALys causes MERRF (Myoclonic Epilepsy with Ragged Red Fibers), a neuromuscular disease. This modified nucleoside of mt tRNALys, recognizes AAA/AAG codons during protein biosynthesis process. Its preference to identify cognate codons has not been studied at the atomic level. Hence, multiple MD simulations of various molecular models of anticodon stem loop (ASL) of mt tRNALys in presence and absence of τm5s2U34 and N6-threonylcarbamoyl adenosine (t6A37) along with AAA and AAG codons have been accomplished. Additional four MD simulations of multiple ASL mt tRNALys models in the context of ribosomal A-site residues have also been performed to investigate the role of A-site in recognition of AAA/AAG codons. MD simulation results show that, ASL models in presence of τm5s2U34 and t6A37 with codons AAA/AAG are more stable than the ASL lacking these modified bases. MD trajectories suggest that τm5s2U recognizes the codons initially by 'wobble' hydrogen bonding interactions, and then tRNALys might leave the explicit codon by a novel 'single' hydrogen bonding interaction in order to run the protein biosynthesis process smoothly. We propose this model as the 'Foot-Step Model' for codon recognition, in which the single hydrogen bond plays a crucial role. MD simulation results suggest that, tRNALys with τm5s2U and t6A recognizes AAA codon more preferably than AAG. Thus, these results reveal the consequences of τm5s2U and t6A in recognition of AAA/AAG codons in mitochondrial disease, MERRF.
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Affiliation(s)
- Kailas D Sonawane
- a Structural Bioinformatics Unit, Department of Biochemistry , Shivaji University , Kolhapur 416 004 (M.S.) , India.,b Department of Microbiology , Shivaji University , Kolhapur 416 004 (M.S.) , India
| | - Asmita S Kamble
- a Structural Bioinformatics Unit, Department of Biochemistry , Shivaji University , Kolhapur 416 004 (M.S.) , India
| | - Prayagraj M Fandilolu
- a Structural Bioinformatics Unit, Department of Biochemistry , Shivaji University , Kolhapur 416 004 (M.S.) , India
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35
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Duchardt-Ferner E, Wöhnert J. NMR experiments for the rapid identification of P=O···H-X type hydrogen bonds in nucleic acids. JOURNAL OF BIOMOLECULAR NMR 2017; 69:101-110. [PMID: 29032519 DOI: 10.1007/s10858-017-0140-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 10/05/2017] [Indexed: 05/24/2023]
Abstract
Hydrogen bonds involving the backbone phosphate groups occur with high frequency in functional RNA molecules. They are often found in well-characterized tertiary structural motifs presenting powerful probes for the rapid identification of these motifs for structure elucidation purposes. We have shown recently that stable hydrogen bonds to the phosphate backbone can in principle be detected by relatively simple NMR-experiments, providing the identity of both the donor hydrogen and the acceptor phosphorous within the same experiment (Duchardt-Ferner et al., Angew Chem Int Ed Engl 50:7927-7930, 2011). However, for imino and hydroxyl hydrogen bond donor groups rapidly exchanging with the solvent as well as amino groups broadened by conformational exchange experimental sensitivity is severely hampered by extensive line broadening. Here, we present improved methods for the rapid identification of hydrogen bonds to phosphate groups in nucleic acids by NMR. The introduction of the SOFAST technique into 1H,31P-correlation experiments as well as a BEST-HNP experiment exploiting 3hJN,P rather than 2hJH,P coupling constants enables the rapid and sensitive identification of these hydrogen bonds in RNA. The experiments are applicable for larger RNAs (up to ~ 100-nt), for donor groups influenced by conformational exchange processes such as amino groups and for hydrogen bonds with rather labile hydrogens such as 2'-OH groups as well as for moderate sample concentrations. Interestingly, the size of the through-hydrogen bond scalar coupling constants depends not only on the type of the donor group but also on the structural context. The largest coupling constants were measured for hydrogen bonds involving the imino groups of protonated cytosine nucleotides as donors.
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Affiliation(s)
- Elke Duchardt-Ferner
- Institute for Molecular Biosciences, Goethe-University, Frankfurt/M., Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University, Frankfurt/M., Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Jens Wöhnert
- Institute for Molecular Biosciences, Goethe-University, Frankfurt/M., Max-von-Laue-Str. 9, 60438, Frankfurt, Germany.
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University, Frankfurt/M., Max-von-Laue-Str. 9, 60438, Frankfurt, Germany.
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36
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Schulz EC, Seiler M, Zuliani C, Voigt F, Rybin V, Pogenberg V, Mücke N, Wilmanns M, Gibson TJ, Barabas O. Intermolecular base stacking mediates RNA-RNA interaction in a crystal structure of the RNA chaperone Hfq. Sci Rep 2017; 7:9903. [PMID: 28852099 PMCID: PMC5575007 DOI: 10.1038/s41598-017-10085-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 08/02/2017] [Indexed: 11/18/2022] Open
Abstract
The RNA-chaperone Hfq catalyses the annealing of bacterial small RNAs (sRNAs) with target mRNAs to regulate gene expression in response to environmental stimuli. Hfq acts on a diverse set of sRNA-mRNA pairs using a variety of different molecular mechanisms. Here, we present an unusual crystal structure showing two Hfq-RNA complexes interacting via their bound RNA molecules. The structure contains two Hfq6:A18 RNA assemblies positioned face-to-face, with the RNA molecules turned towards each other and connected via interdigitating base stacking interactions at the center. Biochemical data further confirm the observed interaction, and indicate that RNA-mediated contacts occur between Hfq-RNA complexes with various (ARN)X motif containing RNA sequences in vitro, including the stress response regulator OxyS and its target, fhlA. A systematic computational survey also shows that phylogenetically conserved (ARN)X motifs are present in a subset of sRNAs, some of which share similar modular architectures. We hypothesise that Hfq can co-opt RNA-RNA base stacking, an unanticipated structural trick, to promote the interaction of (ARN)X motif containing sRNAs with target mRNAs on a “speed-dating” fashion, thereby supporting their regulatory function.
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Affiliation(s)
- Eike C Schulz
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany.,Hamburg Outstation, European Molecular Biology Laboratory, Hamburg, 22603, Germany.,Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Markus Seiler
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany.,Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Str. 15, 60438, Frankfurt a.M., Germany
| | - Cecilia Zuliani
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany
| | - Franka Voigt
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany.,Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland
| | - Vladimir Rybin
- Protein Expression and Purification Core Facility, European Molecular Biology Laboratory, 69117, Heidelberg, Germany
| | - Vivian Pogenberg
- Hamburg Outstation, European Molecular Biology Laboratory, Hamburg, 22603, Germany
| | - Norbert Mücke
- Division Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, 69120, Germany
| | - Matthias Wilmanns
- Hamburg Outstation, European Molecular Biology Laboratory, Hamburg, 22603, Germany
| | - Toby J Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany
| | - Orsolya Barabas
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany.
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37
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Pak D, Root-Bernstein R, Burton ZF. tRNA structure and evolution and standardization to the three nucleotide genetic code. Transcription 2017. [PMID: 28632998 PMCID: PMC5574529 DOI: 10.1080/21541264.2017.1318811] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Cloverleaf tRNA with a 75 nucleotide (nt) core is posited to have evolved from ligation of three 31 nt minihelices followed by symmetric internal deletions of 9 nt within ligated acceptor stems. Statistical tests strongly support the model. Although the tRNA anticodon loop and T loop are homologs, their U-turns have been treated as distinct motifs. An appropriate comparison, however, shows that intercalation of D loop G19 between T loop bases 4 and 5 causes elevation of T loop base 5 and flipping of T loop bases 6 and 7 out of the 7 nt loop. In the anticodon loop, by contrast, loop bases 3–7 stack tightly to form a stiff connection to mRNA. Furthermore, we identify ancient repeat sequences of 3 (GCG), 5 (UAGCC) and 17 nt (∼CCGGGUUCAAAACCCGG) that comprise 75 out of 75 nts of the tRNA cloverleaf core. To present a sufficiently stiff 3-nt anticodon, a 7-nt anticodon loop was necessary with a U-turn between loop positions 2 and 3. Cloverleaf tRNA, therefore, was a radical evolutionary innovation essential for the 3-nt code. Conservation of GCG and UAGCC repeat sequences indicates that cloverleaf tRNA is at the interface between a strange RNA repeat world and the first evolution of molecules that fold to assume biologic functions. We posit that cloverleaf tRNA was the molecular archetype around which translation systems evolved.
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Affiliation(s)
- Daewoo Pak
- a Center for Statistical Training and Consulting , Michigan State University , East Lansing , MI , USA
| | | | - Zachary F Burton
- c Department of Biochemistry and Molecular Biology , Michigan State University , MI , USA
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38
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Väre VYP, Eruysal ER, Narendran A, Sarachan KL, Agris PF. Chemical and Conformational Diversity of Modified Nucleosides Affects tRNA Structure and Function. Biomolecules 2017; 7:E29. [PMID: 28300792 PMCID: PMC5372741 DOI: 10.3390/biom7010029] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 03/06/2017] [Accepted: 03/06/2017] [Indexed: 12/21/2022] Open
Abstract
RNAs are central to all gene expression through the control of protein synthesis. Four major nucleosides, adenosine, guanosine, cytidine and uridine, compose RNAs and provide sequence variation, but are limited in contributions to structural variation as well as distinct chemical properties. The ability of RNAs to play multiple roles in cellular metabolism is made possible by extensive variation in length, conformational dynamics, and the over 100 post-transcriptional modifications. There are several reviews of the biochemical pathways leading to RNA modification, but the physicochemical nature of modified nucleosides and how they facilitate RNA function is of keen interest, particularly with regard to the contributions of modified nucleosides. Transfer RNAs (tRNAs) are the most extensively modified RNAs. The diversity of modifications provide versatility to the chemical and structural environments. The added chemistry, conformation and dynamics of modified nucleosides occurring at the termini of stems in tRNA's cloverleaf secondary structure affect the global three-dimensional conformation, produce unique recognition determinants for macromolecules to recognize tRNAs, and affect the accurate and efficient decoding ability of tRNAs. This review will discuss the impact of specific chemical moieties on the structure, stability, electrochemical properties, and function of tRNAs.
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Affiliation(s)
- Ville Y P Väre
- The RNA Institute, Departments of Biological Sciences and Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA.
| | - Emily R Eruysal
- The RNA Institute, Departments of Biological Sciences and Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA.
| | - Amithi Narendran
- The RNA Institute, Departments of Biological Sciences and Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA.
| | - Kathryn L Sarachan
- The RNA Institute, Departments of Biological Sciences and Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA.
| | - Paul F Agris
- The RNA Institute, Departments of Biological Sciences and Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA.
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39
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D'Ascenzo L, Leonarski F, Vicens Q, Auffinger P. Revisiting GNRA and UNCG folds: U-turns versus Z-turns in RNA hairpin loops. RNA (NEW YORK, N.Y.) 2017; 23:259-269. [PMID: 27999116 PMCID: PMC5311481 DOI: 10.1261/rna.059097.116] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 11/29/2016] [Indexed: 06/06/2023]
Abstract
When thinking about RNA three-dimensional structures, coming across GNRA and UNCG tetraloops is perceived as a boon since their folds have been extensively described. Nevertheless, analyzing loop conformations within RNA and RNP structures led us to uncover several instances of GNRA and UNCG loops that do not fold as expected. We noticed that when a GNRA does not assume its "natural" fold, it adopts the one we typically associate with a UNCG sequence. The same folding interconversion may occur for loops with UNCG sequences, for instance within tRNA anticodon loops. Hence, we show that some structured tetranucleotide sequences starting with G or U can adopt either of these folds. The underlying structural basis that defines these two fold types is the mutually exclusive stacking of a backbone oxygen on either the first (in GNRA) or the last nucleobase (in UNCG), generating an oxygen-π contact. We thereby propose to refrain from using sequences to distinguish between loop conformations. Instead, we suggest using descriptors such as U-turn (for "GNRA-type" folds) and a newly described Z-turn (for "UNCG-type" folds). Because tetraloops adopt for the largest part only two (inter)convertible turns, we are better able to interpret from a structural perspective loop interchangeability occurring in ribosomes and viral RNA. In this respect, we propose a general view on the inclination for a given sequence to adopt (or not) a specific fold. We also suggest how long-noncoding RNAs may adopt discrete but transient structures, which are therefore hard to predict.
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Affiliation(s)
- Luigi D'Ascenzo
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67000 Strasbourg, France
| | - Filip Leonarski
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67000 Strasbourg, France
- Faculty of Chemistry, University of Warsaw, 02-093 Warsaw, Poland
| | - Quentin Vicens
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67000 Strasbourg, France
| | - Pascal Auffinger
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67000 Strasbourg, France
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40
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Abstract
RNA is involved in the regulation of multiple cellular processes, often by forming sequence-specific base pairs with cellular RNA or DNA targets that must be identified among the large number of nucleic acids in a cell. Several RNA-based regulatory systems in eukaryotes, bacteria and archaea, including microRNAs (miRNAs), small interfering RNAs (siRNAs), CRISPR RNAs (crRNAs) and small RNAs (sRNAs) that are dependent on the RNA chaperone protein Hfq, achieve specificity using similar strategies. Central to their function is the presentation of short 'seed sequences' within a ribonucleoprotein complex to facilitate the search for and recognition of targets.
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41
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Maiti S, Bhattacharyya D. Stacking interactions involving non-Watson–Crick basepairs: dispersion corrected density functional theory studies. Phys Chem Chem Phys 2017; 19:28718-28730. [DOI: 10.1039/c7cp04904h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Stacking interactions between a non Watson–Crick G:A S:HT basepair and C:G basepair is predicted in terms of roll, twist and slide basepair step parameters using DFT-D augmented with coarse-grain energy penalty for sugar–phosphate backbone.
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Affiliation(s)
- Satyabrata Maiti
- Computational Science Division
- Saha Institute of Nuclear Physics
- Kolkata 700064
- India
- Homi Bhaba National Institute
| | - Dhananjay Bhattacharyya
- Computational Science Division
- Saha Institute of Nuclear Physics
- Kolkata 700064
- India
- Homi Bhaba National Institute
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42
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Chan RT, Keating KS, Go MC, Toor N. Identification of a GUAAY Pentaloop Sequence Involved in a Novel RNA Loop-Helix Interaction. J Mol Biol 2016; 428:4882-4889. [PMID: 27771480 PMCID: PMC5138090 DOI: 10.1016/j.jmb.2016.10.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 10/11/2016] [Accepted: 10/11/2016] [Indexed: 11/25/2022]
Abstract
Large RNAs often utilize GNRA tetraloops as structural elements to stabilize the overall tertiary fold. These tetraloop-receptor (TR) interactions have a conserved geometry in which the tetraloop docks into the receptor at an angle of ~15° from the helix containing the receptor. Here, we show that the conserved GUAAY pentaloop found in domain III of group IIB1 introns participates in a novel class of RNA tertiary interaction with a geometry and mode of binding that are significantly different from that found in GNRA TR interactions. This pentaloop is highly conserved within the IIB1 class and interacts with the minor groove of the catalytic domain V. The base planes of the loop and receptor nucleotides are not coplanar and greatly deviate from standard A-minor motifs. The helical axis of the GUAAY stem loop diverges ~70° from the angle of insertion found in a typical GNRA TR interaction. Therefore, the loop architecture and insertion orientation are distinctive, with in vitro splicing data indicating that a GNRA tetraloop is incompatible at this position. The GUAAY pentaloop-receptor motif is also found in the structure of the eukaryotic thiamine pyrophosphate riboswitch in the context of a hexanucleotide loop sequence. We therefore propose, based on phylogenetic, structural, and biochemical data, that the GUAAY pentaloop-receptor interaction represents a novel structural motif that is present in multiple structured RNAs.
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Affiliation(s)
- Russell T Chan
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
| | | | - Michaela C Go
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Navtej Toor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA.
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43
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Börner R, Kowerko D, Miserachs HG, Schaffer MF, Sigel RK. Metal ion induced heterogeneity in RNA folding studied by smFRET. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2016.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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44
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Welty R, Hall KB. Nucleobases Undergo Dynamic Rearrangements during RNA Tertiary Folding. J Mol Biol 2016; 428:4490-4502. [PMID: 27693721 DOI: 10.1016/j.jmb.2016.09.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 08/31/2016] [Accepted: 09/15/2016] [Indexed: 02/07/2023]
Abstract
The tertiary structure of the GTPase center (GAC) of 23S ribosomal RNA (rRNA) as seen in cocrystals is extremely compact. It is stabilized by long-range hydrogen bonds and nucleobase stacking and by a triloop that forms within its three-way junction. Its folding pathway from secondary structure to tertiary structure has not been previously observed, but it was shown to require Mg2+ ions in equilibrium experiments. The fluorescent nucleotide 2-aminopurine was substituted at selected sites within the 60-nt GAC. Fluorescence intensity changes upon addition of MgCl2 were monitored over a time-course from 1ms to 100s as the RNA folds. The folding pathway is revealed here to be hierarchical through several intermediates. Observation of the nucleobases during folding provides a new perspective on the process and the pathway, revealing the dynamics of nucleobase conformational exchange during the folding transitions.
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Affiliation(s)
- Robb Welty
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Kathleen B Hall
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA.
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45
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Zhou M, Long T, Fang ZP, Zhou XL, Liu RJ, Wang ED. Identification of determinants for tRNA substrate recognition by Escherichia coli C/U34 2'-O-methyltransferase. RNA Biol 2016; 12:900-11. [PMID: 26106808 PMCID: PMC4615657 DOI: 10.1080/15476286.2015.1050576] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Post-transcriptional modifications bring chemical diversity to tRNAs, especially at positions 34 and 37 of the anticodon stem-loop (ASL). TrmL is the prokaryotic methyltransferase that catalyzes the transfer of the methyl group from S-adenosyl-L-methionine to the wobble base of tRNALeuCAA and tRNALeuUAA isoacceptors. This Cm34/Um34 modification affects codon-anticodon interactions and is essential for translational fidelity. TrmL-catalyzed 2′-O-methylation requires its homodimerization; however, understanding of the tRNA recognition mechanism by TrmL remains elusive. In the current study, by measuring tRNA methylation by TrmL and performing kinetic analysis of tRNA mutants, we found that TrmL exhibits a fine-tuned tRNA substrate recognition mechanism. Anticodon stem-loop minihelices with an extension of 2 base pairs are the minimal substrate for EcTrmL methylation. A35 is a key residue for TrmL recognition, while A36-A37-A38 are important either via direct interaction with TrmL or due to the necessity for prior isopentenylation (i6) at A37. In addition, TrmL only methylates pyrimidines but not purine residues at the wobble position, and the 2′-O-methylation relies on prior N6-isopentenyladenosine modification at position 37.
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Affiliation(s)
- Mi Zhou
- a State Key Laboratory of Molecular Biology ; Institute of Biochemistry and Cell Biology; Shanghai Institutes for Biological Sciences ; Chinese Academy of Sciences ; Shanghai , PR China
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46
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Comparative Structural Dynamics of tRNA(Phe) with Respect to Hinge Region Methylated Guanosine: A Computational Approach. Cell Biochem Biophys 2016; 74:157-73. [PMID: 27216172 DOI: 10.1007/s12013-016-0731-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 05/01/2016] [Indexed: 12/13/2022]
Abstract
Transfer RNAs (tRNAs) contain various uniquely modified nucleosides thought to be useful for maintaining the structural stability of tRNAs. However, their significance for upholding the tRNA structure has not been investigated in detail at the atomic level. In this study, molecular dynamic simulations have been performed to assess the effects of methylated nucleic acid bases, N (2)-methylguanosine (m(2)G) and N (2)-N (2)-dimethylguanosine (m 2 (2) G) at position 26, i.e., the hinge region of E. coli tRNA(Phe) on its structure and dynamics. The results revealed that tRNA(Phe) having unmodified guanosine in the hinge region (G26) shows structural rearrangement in the core of the molecule, resulting in lack of base stacking interactions, U-turn feature of the anticodon loop, and TΨC loop. We show that in the presence of the unmodified guanosine, the overall fold of tRNA(Phe) is essentially not the same as that of m(2)G26 and m 2 (2) G26 containing tRNA(Phe). This structural rearrangement arises due to intrinsic factors associated with the weak hydrogen-bonding patterns observed in the base triples of the tRNA(Phe) molecule. The m(2)G26 and m 2 (2) G26 containing tRNA(Phe) retain proper three-dimensional fold through tertiary interactions. Single-point energy and molecular electrostatics potential calculation studies confirmed the structural significance of tRNAs containing m(2)G26 and m 2 (2) G26 compared to tRNA with normal G26, showing that the mono-methylated (m(2)G26) and dimethylated (m 2 (2) G26) modifications are required to provide structural stability not only in the hinge region but also in the other parts of tRNA(Phe). Thus, the present study allows us to better understand the effects of modified nucleosides and ionic environment on tRNA folding.
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47
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Draper DE. Folding of RNA tertiary structure: Linkages between backbone phosphates, ions, and water. Biopolymers 2016; 99:1105-13. [PMID: 23568785 DOI: 10.1002/bip.22249] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 03/14/2013] [Accepted: 03/25/2013] [Indexed: 01/08/2023]
Abstract
The functional forms of many RNAs have compact architectures. The placement of phosphates within such structures must be influenced not only by the strong electrostatic repulsion between phosphates, but also by networks of interactions between phosphates, water, and mobile ions. This review first explores what has been learned of the basic thermodynamic constraints on these arrangements from studies of hydration and ions in simple DNA molecules, and then gives an overview of what is known about ion and water interactions with RNA structures. A brief survey of RNA crystal structures identifies several interesting architectures in which closely spaced phosphates share hydration shells or phosphates are buried in environments that provide intramolecular hydrogen bonds or site-bound cations. Formation of these structures must require strong coupling between the uptake of ions and release of water.
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Affiliation(s)
- David E Draper
- Departments of Chemistry and Biophysics, Johns Hopkins University, Baltimore, MD, 21218
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48
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Ogawa T. tRNA-targeting ribonucleases: molecular mechanisms and insights into their physiological roles. Biosci Biotechnol Biochem 2016; 80:1037-45. [PMID: 26967967 DOI: 10.1080/09168451.2016.1148579] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Most bacteria produce antibacterial proteins known as bacteriocins, which aid bacterial defence systems to provide a physiological advantage. To date, many kinds of bacteriocins have been characterized. Colicin has long been known as a plasmidborne bacteriocin that kills other Escherichia coli cells lacking the same plasmid. To defeat other cells, colicins exert specific activities such as ion-channel, DNase, and RNase activity. Colicin E5 and colicin D impair protein synthesis in sensitive E. coli cells; however, their physiological targets have not long been identified. This review describes our finding that colicins E5 and D are novel RNases targeting specific E. coli tRNAs and elucidates their enzymatic properties based on biochemical analyses and X-ray crystal structures. Moreover, tRNA cleavage mediates bacteriostasis, which depends on trans-translation. Based on these results and others, cell growth regulation depending on tRNA cleavage is also discussed.
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Affiliation(s)
- Tetsuhiro Ogawa
- a Department of Biotechnology , The University of Tokyo , Tokyo , Japan
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49
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Gupta A, Bansal M. The role of sequence in altering the unfolding pathway of an RNA pseudoknot: a steered molecular dynamics study. Phys Chem Chem Phys 2016; 18:28767-28780. [DOI: 10.1039/c6cp04617g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
This work highlights a sequence dependent unfolding pathway of an RNA pseudoknot under force-induced pulling conditions.
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Affiliation(s)
- Asmita Gupta
- Molecular Biophysics Unit
- Indian Institute of Science
- Bangalore-560012
- India
| | - Manju Bansal
- Molecular Biophysics Unit
- Indian Institute of Science
- Bangalore-560012
- India
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50
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Bou-Nader C, Pecqueur L, Bregeon D, Kamah A, Guérineau V, Golinelli-Pimpaneau B, Guimarães BG, Fontecave M, Hamdane D. An extended dsRBD is required for post-transcriptional modification in human tRNAs. Nucleic Acids Res 2015; 43:9446-56. [PMID: 26429968 PMCID: PMC4627097 DOI: 10.1093/nar/gkv989] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 09/19/2015] [Indexed: 12/25/2022] Open
Abstract
In tRNA, dihydrouridine is a conserved modified base generated by the post-transcriptional reduction of uridine. Formation of dihydrouridine 20, located in the D-loop, is catalyzed by dihydrouridine synthase 2 (Dus2). Human Dus2 (HsDus2) expression is upregulated in lung cancers, offering a growth advantage throughout its ability to interact with components of the translation apparatus and inhibit apoptosis. Here, we report the crystal structure of the individual domains of HsDus2 and their functional characterization. HsDus2 is organized into three major modules. The N-terminal catalytic domain contains the flavin cofactor involved in the reduction of uridine. The second module is the conserved α-helical domain known as the tRNA binding domain in HsDus2 homologues. It is connected via a flexible linker to an unusual extended version of a dsRNA binding domain (dsRBD). Enzymatic assays and yeast complementation showed that the catalytic domain binds selectively NADPH but cannot reduce uridine in the absence of the dsRBD. While in Dus enzymes from bacteria, plants and fungi, tRNA binding is essentially achieved by the α-helical domain, we showed that in HsDus2 this function is carried out by the dsRBD. This is the first reported case of a tRNA-modifying enzyme carrying a dsRBD used to bind tRNAs.
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Affiliation(s)
- Charles Bou-Nader
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, France, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Ludovic Pecqueur
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, France, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Damien Bregeon
- Sorbonne Universités, UPMC Univ. Paris 06, IBPS, UMR8256, Biology of Aging and Adaptation, F-75005 Paris, France
| | - Amina Kamah
- Université de Lille-Nord de France, CNRS UMR 8576, Institut Fédératif de Recherches 147, Villeneuve d'Ascq, France
| | - Vincent Guérineau
- Institut de Chimie des Substances Naturelles, Centre de Recherche de Gif, CNRS, 1 avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Béatrice Golinelli-Pimpaneau
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, France, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Beatriz G Guimarães
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, 91190 Gif-sur-Yvette, France
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, France, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Djemel Hamdane
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, France, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
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