1
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Ding D, Fang Z, Kim SC, O’Flaherty DK, Jia X, Stone TB, Zhou L, Szostak JW. Unusual Base Pair between Two 2-Thiouridines and Its Implication for Nonenzymatic RNA Copying. J Am Chem Soc 2024; 146:3861-3871. [PMID: 38293747 PMCID: PMC10870715 DOI: 10.1021/jacs.3c11158] [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: 10/09/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 02/01/2024]
Abstract
2-Thiouridine (s2U) is a nucleobase modification that confers enhanced efficiency and fidelity both on modern tRNA codon translation and on nonenzymatic and ribozyme-catalyzed RNA copying. We have discovered an unusual base pair between two 2-thiouridines that stabilizes an RNA duplex to a degree that is comparable to that of a native A:U base pair. High-resolution crystal structures indicate similar base-pairing geometry and stacking interactions in duplexes containing s2U:s2U compared to those with U:U pairs. Notably, the C═O···H-N hydrogen bond in the U:U pair is replaced with a C═S···H-N hydrogen bond in the s2U:s2U base pair. The thermodynamic stability of the s2U:s2U base pair suggested that this self-pairing might lead to an increased error frequency during nonenzymatic RNA copying. However, competition experiments show that s2U:s2U base-pairing induces only a low level of misincorporation during nonenzymatic RNA template copying because the correct A:s2U base pair outcompetes the slightly weaker s2U:s2U base pair. In addition, even if an s2U is incorrectly incorporated, the addition of the next base is greatly hindered. This strong stalling effect would further increase the effective fidelity of nonenzymatic RNA copying with s2U. Our findings suggest that s2U may enhance the rate and extent of nonenzymatic copying with only a minimal cost in fidelity.
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Affiliation(s)
- Dian Ding
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
- Department
of Molecular Biology and Center for Computational and Integrative
Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - Ziyuan Fang
- Howard
Hughes Medical Institute, Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Seohyun Chris Kim
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
- Department
of Molecular Biology and Center for Computational and Integrative
Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Department
of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Derek K. O’Flaherty
- Department
of Chemistry, College of Engineering and Physical Sciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Xiwen Jia
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
- Department
of Molecular Biology and Center for Computational and Integrative
Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - Talbot B. Stone
- Department
of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Penn
Institute for RNA Innovation, University
of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Lijun Zhou
- Department
of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Penn
Institute for RNA Innovation, University
of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Jack W. Szostak
- Howard
Hughes Medical Institute, Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
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2
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Haruehanroengra P, Zheng YY, Ma G, Lan TH, Hassan AEA, Zhou Y, Sheng J. Probing the Substrate Requirements of the in vitro Geranylation Activity of Selenouridine Synthase (SelU). Chembiochem 2022; 23:e202200089. [DOI: 10.1002/cbic.202200089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 05/31/2022] [Indexed: 11/10/2022]
Affiliation(s)
| | - Ya Ying Zheng
- University at Albany Chemistry 1400 Washington Ave.Life Science 2033B 12222 Albany UNITED STATES
| | - Guolin Ma
- Texas A&M University System Health Science Center College of Medicine: Texas A&M University College of Medicine Bioscience and Technology UNITED STATES
| | - Tien-Hung Lan
- Texas A&M University System Health Science Center College of Medicine: Texas A&M University College of Medicine Bioscience and Technology UNITED STATES
| | | | - Yubin Zhou
- Texas A&M University System Health Science Center College of Medicine: Texas A&M University College of Medicine Bioscience and Technology UNITED STATES
| | - Jia Sheng
- University at Albany State University of New York Chemistry 1400 Washington Ave.LSRB 2033B 12222 Albany UNITED STATES
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3
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D’Esposito RJ, Myers CA, Chen AA, Vangaveti S. Challenges with Simulating Modified RNA: Insights into Role and Reciprocity of Experimental and Computational Approaches. Genes (Basel) 2022; 13:genes13030540. [PMID: 35328093 PMCID: PMC8949676 DOI: 10.3390/genes13030540] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 01/12/2023] Open
Abstract
RNA is critical to a broad spectrum of biological and viral processes. This functional diversity is a result of their dynamic nature; the variety of three-dimensional structures that they can fold into; and a host of post-transcriptional chemical modifications. While there are many experimental techniques to study the structural dynamics of biomolecules, molecular dynamics simulations (MDS) play a significant role in complementing experimental data and providing mechanistic insights. The accuracy of the results obtained from MDS is determined by the underlying physical models i.e., the force-fields, that steer the simulations. Though RNA force-fields have received a lot of attention in the last decade, they still lag compared to their protein counterparts. The chemical diversity imparted by the RNA modifications adds another layer of complexity to an already challenging problem. Insight into the effect of RNA modifications upon RNA folding and dynamics is lacking due to the insufficiency or absence of relevant experimental data. This review provides an overview of the state of MDS of modified RNA, focusing on the challenges in parameterization of RNA modifications as well as insights into relevant reference experiments necessary for their calibration.
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Affiliation(s)
- Rebecca J. D’Esposito
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA; (R.J.D.); (A.A.C.)
| | - Christopher A. Myers
- Department of Physics, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA;
| | - Alan A. Chen
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA; (R.J.D.); (A.A.C.)
- The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA
| | - Sweta Vangaveti
- The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA
- Correspondence:
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4
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Jia TZ, Nishikawa S, Fujishima K. Sequencing the Origins of Life. BBA ADVANCES 2022; 2:100049. [PMID: 37082609 PMCID: PMC10074849 DOI: 10.1016/j.bbadva.2022.100049] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/27/2022] [Accepted: 03/02/2022] [Indexed: 01/10/2023] Open
Abstract
One goal of origins of life research is to understand how primitive informational and catalytic biopolymers emerged and evolved. Recently, a number of sequencing techniques have been applied to analysis of replicating and evolving primitive biopolymer systems, providing a sequence-specific and high-resolution view of primitive chemical processes. Here, we review application of sequencing techniques to analysis of synthetic and primitive nucleic acids and polypeptides. This includes next-generation sequencing of primitive polymerization and evolution processes, followed by discussion of other novel biochemical techniques that could contribute to sequence analysis of primitive biopolymer driven chemical systems. Further application of sequencing to origins of life research, perhaps as a life detection technology, could provide insight into the origin and evolution of informational and catalytic biopolymers on early Earth or elsewhere.
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Affiliation(s)
- Tony Z. Jia
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Blue Marble Space Institute of Science, 600 1st Ave, Floor 1, Seattle, WA 98104, USA
- Corresponding author
| | - Shota Nishikawa
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan
| | - Kosuke Fujishima
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa-shi, Kanagawa 252-0882, Japan
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5
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Ding D, Zhou L, Giurgiu C, Szostak JW. Kinetic explanations for the sequence biases observed in the nonenzymatic copying of RNA templates. Nucleic Acids Res 2021; 50:35-45. [PMID: 34893864 PMCID: PMC8754633 DOI: 10.1093/nar/gkab1202] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/17/2021] [Accepted: 12/08/2021] [Indexed: 11/15/2022] Open
Abstract
The identification of nonenzymatic pathways for nucleic acid replication is a key challenge in understanding the origin of life. We have previously shown that nonenzymatic RNA primer extension using 2-aminoimidazole (2AI) activated nucleotides occurs primarily through an imidazolium-bridged dinucleotide intermediate. The reactive nature and preorganized structure of the intermediate increase the efficiency of primer extension but remain insufficient to drive extensive copying of RNA templates containing all four canonical nucleotides. To understand the factors that limit RNA copying, we synthesized all ten 2AI-bridged dinucleotide intermediates and measured the kinetics of primer extension in a model system. The affinities of the ten dinucleotides for the primer/template/helper complexes vary by over 7,000-fold, consistent with nearest neighbor energetic predictions. Surprisingly, the reaction rates at saturating intermediate concentrations still vary by over 15-fold, with the most weakly binding dinucleotides exhibiting a lower maximal reaction rate. Certain noncanonical nucleotides can decrease sequence dependent differences in affinity and primer extension rate, while monomers bridged to short oligonucleotides exhibit enhanced binding and reaction rates. We suggest that more uniform binding and reactivity of imidazolium-bridged intermediates may lead to the ability to copy arbitrary template sequences under prebiotically plausible conditions.
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Affiliation(s)
- Dian Ding
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, USA.,Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
| | - Lijun Zhou
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, USA.,Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
| | - Constantin Giurgiu
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, USA.,Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, USA.,Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA.,Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
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6
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Heidari A, Hermann M, Hudson RHE. A simple fluorescent assay for the detection of peptide nucleic acid-directed double strand duplex invasion. Biopolymers 2021; 113:e23475. [PMID: 34529824 DOI: 10.1002/bip.23475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 08/24/2021] [Accepted: 08/30/2021] [Indexed: 11/06/2022]
Abstract
Peptide nucleic acid (PNA) is a mimic of nucleic acids that is able to bind complementary oligonucleotides with high affinity and excellent selectivity. As such, the use of PNA has been proposed in numerous applications in biochemistry, medicine, and biotechnology. Sequences of pseudo-complementary PNAs containing diaminopurine (D)-2-thiouracil (S U) base pairs bind to complementary regions within double-stranded DNA targets. This type of binding is termed "double duplex invasion" and involves unwinding of the duplex accompanied by simultaneous hybridization of both DNA strands by the two pseudo-complementary PNAs. In this study, a simple method of assaying DNA strand invasion by pseudo-complementary PNAs was developed. This method is based on the incorporation of a single fluorescent cytidine analog, phenylpyrrolocytidine (PhpC), into the double-stranded DNA target such that upon invasion by PNA, the PhpC is displaced to a single-stranded region resulting in the turn-on of fluorescence emission. This fluorescent assay is applicable to studies both at equilibrium and approach-to-equilibrium (time-dependent) conditions.
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Affiliation(s)
- Ali Heidari
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada
| | - Mason Hermann
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada
| | - Robert H E Hudson
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada
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7
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Zheng YY, Wu Y, Begley TJ, Sheng J. Sulfur modification in natural RNA and therapeutic oligonucleotides. RSC Chem Biol 2021; 2:990-1003. [PMID: 34458821 PMCID: PMC8341892 DOI: 10.1039/d1cb00038a] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 04/22/2021] [Indexed: 11/21/2022] Open
Abstract
Sulfur modifications have been discovered on both DNA and RNA. Sulfur substitution of oxygen atoms at nucleobase or backbone locations in the nucleic acid framework led to a wide variety of sulfur-modified nucleosides and nucleotides. While the discovery, regulation and functions of DNA phosphorothioate (PS) modification, where one of the non-bridging oxygen atoms is replaced by sulfur on the DNA backbone, are important topics, this review focuses on the sulfur modification in natural cellular RNAs and therapeutic nucleic acids. The sulfur modifications on RNAs exhibit diversity in terms of modification location and cellular function, but the various sulfur modifications share common biosynthetic strategies across RNA species, cell types and domains of life. The first section reviews the post-transcriptional sulfur modifications on nucleobases with an emphasis on thiouridine on tRNA and phosphorothioate modification on RNA backbones, as well as the functions of the sulfur modifications on different species of cellular RNAs. The second section reviews the biosynthesis of different types of sulfur modifications and summarizes the general strategy for the biosynthesis of sulfur-containing RNA residues. One of the main goals of investigating sulfur modifications is to aid the genomic drug development pipeline and enhance our understandings of the rapidly growing nucleic acid-based gene therapies. The last section of the review focuses on the current drug development strategies employing sulfur substitution of oxygen atoms in therapeutic RNAs.
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Affiliation(s)
- Ya Ying Zheng
- Department of Chemistry, University at Albany, State University of New York 1400 Washington Ave. Albany NY 12222 USA
- The RNA Institute, University at Albany, State University of New York 1400 Washington Ave. Albany NY 12222 USA
| | - Ying Wu
- Department of Chemistry, University at Albany, State University of New York 1400 Washington Ave. Albany NY 12222 USA
- The RNA Institute, University at Albany, State University of New York 1400 Washington Ave. Albany NY 12222 USA
| | - Thomas J Begley
- The RNA Institute, University at Albany, State University of New York 1400 Washington Ave. Albany NY 12222 USA
- Department of Biological Science, University at Albany, State University of New York 1400 Washington Ave. Albany NY 12222 USA
| | - Jia Sheng
- Department of Chemistry, University at Albany, State University of New York 1400 Washington Ave. Albany NY 12222 USA
- The RNA Institute, University at Albany, State University of New York 1400 Washington Ave. Albany NY 12222 USA
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8
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Duzdevich D, Carr CE, Ding D, Zhang SJ, Walton TS, Szostak JW. Competition between bridged dinucleotides and activated mononucleotides determines the error frequency of nonenzymatic RNA primer extension. Nucleic Acids Res 2021; 49:3681-3691. [PMID: 33744957 PMCID: PMC8053118 DOI: 10.1093/nar/gkab173] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 02/12/2021] [Accepted: 03/05/2021] [Indexed: 12/15/2022] Open
Abstract
Nonenzymatic copying of RNA templates with activated nucleotides is a useful model for studying the emergence of heredity at the origin of life. Previous experiments with defined-sequence templates have pointed to the poor fidelity of primer extension as a major problem. Here we examine the origin of mismatches during primer extension on random templates in the simultaneous presence of all four 2-aminoimidazole-activated nucleotides. Using a deep sequencing approach that reports on millions of individual template-product pairs, we are able to examine correct and incorrect polymerization as a function of sequence context. We have previously shown that the predominant pathway for primer extension involves reaction with imidazolium-bridged dinucleotides, which form spontaneously by the reaction of two mononucleotides with each other. We now show that the sequences of correctly paired products reveal patterns that are expected from the bridged dinucleotide mechanism, whereas those associated with mismatches are consistent with direct reaction of the primer with activated mononucleotides. Increasing the ratio of bridged dinucleotides to activated mononucleotides, either by using purified components or by using isocyanide-based activation chemistry, reduces the error frequency. Our results point to testable strategies for the accurate nonenzymatic copying of arbitrary RNA sequences.
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Affiliation(s)
- Daniel Duzdevich
- To whom correspondence should be addressed. Tel: +1 617 726 5102; Fax: +1 617 643 332;
| | - Christopher E Carr
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Dian Ding
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Stephanie J Zhang
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Travis S Walton
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jack W Szostak
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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9
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Kim SC, O'Flaherty DK, Giurgiu C, Zhou L, Szostak JW. The Emergence of RNA from the Heterogeneous Products of Prebiotic Nucleotide Synthesis. J Am Chem Soc 2021; 143:3267-3279. [PMID: 33636080 DOI: 10.1021/jacs.0c12955] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recent advances in prebiotic chemistry are beginning to outline plausible pathways for the synthesis of the canonical ribonucleotides and their assembly into oligoribonucleotides. However, these reaction pathways suggest that many noncanonical nucleotides are likely to have been generated alongside the standard ribonucleotides. Thus, the oligomerization of prebiotically synthesized nucleotides is likely to have led to a highly heterogeneous collection of oligonucleotides comprised of a wide range of types of nucleotides connected by a variety of backbone linkages. How then did relatively homogeneous RNA emerge from this primordial heterogeneity? Here we focus on nonenzymatic template-directed primer extension as a process that would have strongly enriched for homogeneous RNA over the course of multiple cycles of replication. We review the effects on copying the kinetics of nucleotides with altered nucleobase and sugar moieties, when they are present as activated monomers and when they are incorporated into primer and template oligonucleotides. We also discuss three variations in backbone connectivity, all of which are nonheritable and regenerate native RNA upon being copied. The kinetic superiority of RNA synthesis suggests that nonenzymatic copying served as a chemical selection mechanism that allowed relatively homogeneous RNA to emerge from a complex mixture of prebiotically synthesized nucleotides and oligonucleotides.
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Affiliation(s)
- Seohyun Chris Kim
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Derek K O'Flaherty
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Constantin Giurgiu
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Lijun Zhou
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
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10
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Haruehanroengra P, Vangaveti S, Ranganathan SV, Mao S, Su MD, Chen AA, Sheng J. Terpene Chain Length Affects the Base Pairing Discrimination of S-geranyl-2-thiouridine in RNA Duplex. iScience 2020; 23:101866. [PMID: 33319183 PMCID: PMC7726334 DOI: 10.1016/j.isci.2020.101866] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 10/16/2020] [Accepted: 11/20/2020] [Indexed: 12/20/2022] Open
Abstract
Geranylation is a hydrophobic modification discovered in several bacteria tRNAs with the function of promoting codon bias during translation. However, why nature selects this C10-geranyl group remains a question. We conduct synthesis, UV-thermal denaturation, and molecular simulation studies in RNA duplexes and reveal possible reasons behind this natural selection. Among methyl-(C1), dimethylallyl-(C5), geranyl-(C10), and farnesyl-(C15) modified 2-thiouridines, only geranyl-group promotes U:G over U:A pair. Molecular simulation shows all the modified terpene groups point to the minor groove of RNA duplexes. The discrimination between U:G and U:A pairs derives from the difference in hydrogen bonding and interactions of the chain with the hydrophobic area in the minor groove. Geranyl group has perfect length to discriminate U:G and U:A pairs, whereas the others are either too long or too short to achieve the same behavior. This work indicates that geranyl group cannot be replaced by other terpene groups in promoting codon-specificity. Geranyl group on ges2U has perfect length to enhance binding to G over A in RNA Other ges2U analogues has no pairing preference between G or A MD shows the molecular dynamic behavior of different terpene chains in RNA duplex
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Affiliation(s)
- Phensinee Haruehanroengra
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA.,The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Sweta Vangaveti
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | | | - Song Mao
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA.,The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Max Daniel Su
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA.,The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Alan A Chen
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA.,The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Jia Sheng
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA.,The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
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11
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Wolff P, Villette C, Zumsteg J, Heintz D, Antoine L, Chane-Woon-Ming B, Droogmans L, Grosjean H, Westhof E. Comparative patterns of modified nucleotides in individual tRNA species from a mesophilic and two thermophilic archaea. RNA (NEW YORK, N.Y.) 2020; 26:1957-1975. [PMID: 32994183 PMCID: PMC7668247 DOI: 10.1261/rna.077537.120] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 09/09/2020] [Indexed: 05/22/2023]
Abstract
To improve and complete our knowledge of archaeal tRNA modification patterns, we have identified and compared the modification pattern (type and location) in tRNAs of three very different archaeal species, Methanococcus maripaludis (a mesophilic methanogen), Pyrococcus furiosus (a hyperthermophile thermococcale), and Sulfolobus acidocaldarius (an acidophilic thermophilic sulfolobale). Most abundant isoacceptor tRNAs (79 in total) for each of the 20 amino acids were isolated by two-dimensional gel electrophoresis followed by in-gel RNase digestions. The resulting oligonucleotide fragments were separated by nanoLC and their nucleotide content analyzed by mass spectrometry (MS/MS). Analysis of total modified nucleosides obtained from complete digestion of bulk tRNAs was also performed. Distinct base- and/or ribose-methylations, cytidine acetylations, and thiolated pyrimidines were identified, some at new positions in tRNAs. Novel, some tentatively identified, modifications were also found. The least diversified modification landscape is observed in the mesophilic Methanococcus maripaludis and the most complex one in Sulfolobus acidocaldarius Notable observations are the frequent occurrence of ac4C nucleotides in thermophilic archaeal tRNAs, the presence of m7G at positions 1 and 10 in Pyrococcus furiosus tRNAs, and the use of wyosine derivatives at position 37 of tRNAs, especially those decoding U1- and C1-starting codons. These results complete those already obtained by others with sets of archaeal tRNAs from Methanocaldococcus jannaschii and Haloferax volcanii.
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Affiliation(s)
- Philippe Wolff
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, F-67084, Strasbourg, France
| | - Claire Villette
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, F-67084, Strasbourg, France
| | - Julie Zumsteg
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, F-67084, Strasbourg, France
| | - Dimitri Heintz
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, F-67084, Strasbourg, France
| | - Laura Antoine
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, F-67084, Strasbourg, France
| | - Béatrice Chane-Woon-Ming
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, F-67084, Strasbourg, France
| | - Louis Droogmans
- Laboratoire de Chimie Biologique, Université Libre de Bruxelles, Institut Labiris, B-1070, Belgium
| | - Henri Grosjean
- Laboratoire de Chimie Biologique, Université Libre de Bruxelles, Institut Labiris, B-1070, Belgium
| | - Eric Westhof
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, F-67084, Strasbourg, France
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12
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Sahoo DK, Chand A, Jena S, Biswal HS. Hydrogen-bond-driven thiouracil dissolution in aqueous ionic liquid: A combined microscopic, spectroscopic and molecular dynamics study. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.114275] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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13
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Fernandes De Abreu DA, Salinas-Giegé T, Drouard L, Remy JJ. Alanine tRNAs Translate Environment Into Behavior in Caenorhabditis elegans. Front Cell Dev Biol 2020; 8:571359. [PMID: 33195203 PMCID: PMC7662486 DOI: 10.3389/fcell.2020.571359] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 10/12/2020] [Indexed: 12/16/2022] Open
Abstract
Caenorhabditis elegans nematodes produce and maintain imprints of attractive chemosensory cues to which they are exposed early in life. Early odor-exposure increases adult chemo-attraction to the same cues. Imprinting is transiently or stably inherited, depending on the number of exposed generations. We show here that the Alanine tRNA (UGC) plays a central role in regulating C. elegans chemo-attraction. Naive worms fed on tRNAAla (UGC) purified from odor-experienced worms, acquire odor-specific imprints. Chemo-attractive responses require the tRNA-modifying Elongator complex sub-units 1 (elpc-1) and 3 (elpc-3) genes. elpc-3 deletions impair chemo-attraction, which is fully restored by wild-type tRNAAla (UGC) feeding. A stably inherited decrease of odor-specific responses ensues from early odor-exposition of elpc-1 deletion mutants. tRNAAla (UGC) may adopt various chemical forms to mediate the cross-talk between innately-programmed and environment-directed chemo-attractive behavior.
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Affiliation(s)
- Diana Andrea Fernandes De Abreu
- Genes, Environment, Plasticity, Institut Sophia Agrobiotech ISA UMR CNRS 7254, INRAE 1355, Université Nice Côte d’Azur, Sophia-Antipolis, France
| | - Thalia Salinas-Giegé
- Institut de Biologie Moléculaire des Plantes-CNRS, Université de Strasbourg, Strasbourg, France
| | - Laurence Drouard
- Institut de Biologie Moléculaire des Plantes-CNRS, Université de Strasbourg, Strasbourg, France
| | - Jean-Jacques Remy
- Genes, Environment, Plasticity, Institut Sophia Agrobiotech ISA UMR CNRS 7254, INRAE 1355, Université Nice Côte d’Azur, Sophia-Antipolis, France
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14
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Sarkar AK, Sarzynska J, Lahiri A. Ensemble Allosteric Model for the Modified Wobble Hypothesis. J Phys Chem Lett 2020; 11:6337-6343. [PMID: 32701298 DOI: 10.1021/acs.jpclett.0c00854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The residue 2-thiouridine (s2U) provides a remarkable example for the "modified wobble" hypothesis, which postulates that some post-transcriptional modifications at the wobble position of tRNAs restrict recognition of degenerate codons. Through extensive molecular dynamics simulations using our χIDRP force field parameters, we demonstrate how this modification shifts the conformational ensemble from a predominantly disordered, as in the case of an RNA pentamer (GUUUC), to a substantially ordered population in Gs2UUUC. Our simulations clearly showed that the van der Waals interaction of sulfur played a major role in driving the disorder-to-order transition. The conformational redistribution and the slowing down of the transition between the clusters within the population in the presence of s2U suggest ensemble allostery to be a key mechanism that may play a general role in the functioning of the wobble modifications of tRNAs.
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Affiliation(s)
- Aditya K Sarkar
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata 700 009, India
| | - Joanna Sarzynska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Ansuman Lahiri
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata 700 009, India
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15
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C5-Substituted 2-Selenouridines Ensure Efficient Base Pairing with Guanosine; Consequences for Reading the NNG-3' Synonymous mRNA Codons. Int J Mol Sci 2020; 21:ijms21082882. [PMID: 32326096 PMCID: PMC7216251 DOI: 10.3390/ijms21082882] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/16/2020] [Accepted: 04/18/2020] [Indexed: 12/14/2022] Open
Abstract
5-Substituted 2-selenouridines (R5Se2U) are post-transcriptional modifications present in the first anticodon position of transfer RNA. Their functional role in the regulation of gene expression is elusive. Here, we present efficient syntheses of 5-methylaminomethyl-2-selenouridine (1, mnm5Se2U), 5-carboxymethylaminomethyl-2-selenouridine (2, cmnm5Se2U), and Se2U (3) alongside the crystal structure of the latter nucleoside. By using pH-dependent potentiometric titration, pKa values for the N3H groups of 1–3 were assessed to be significantly lower compared to their 2-thio- and 2-oxo-congeners. At physiological conditions (pH 7.4), Se2-uridines 1 and 2 preferentially adopted the zwitterionic form (ZI, ca. 90%), with the positive charge located at the amino alkyl side chain and the negative charge at the Se2-N3-O4 edge. As shown by density functional theory (DFT) calculations, this ZI form efficiently bound to guanine, forming the so-called “new wobble base pair”, which was accepted by the ribosome architecture. These data suggest that the tRNA anticodons with wobble R5Se2Us may preferentially read the 5′-NNG-3′ synonymous codons, unlike their 2-thio- and 2-oxo-precursors, which preferentially read the 5′-NNA-3′ codons. Thus, the interplay between the levels of U-, S2U- and Se2U-tRNA may have a dominant role in the epitranscriptomic regulation of gene expression via reading of the synonymous 3′-A- and 3′-G-ending codons.
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16
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McCown PJ, Ruszkowska A, Kunkler CN, Breger K, Hulewicz JP, Wang MC, Springer NA, Brown JA. Naturally occurring modified ribonucleosides. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 11:e1595. [PMID: 32301288 PMCID: PMC7694415 DOI: 10.1002/wrna.1595] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 03/09/2020] [Accepted: 03/11/2020] [Indexed: 12/18/2022]
Abstract
The chemical identity of RNA molecules beyond the four standard ribonucleosides has fascinated scientists since pseudouridine was characterized as the “fifth” ribonucleotide in 1951. Since then, the ever‐increasing number and complexity of modified ribonucleosides have been found in viruses and throughout all three domains of life. Such modifications can be as simple as methylations, hydroxylations, or thiolations, complex as ring closures, glycosylations, acylations, or aminoacylations, or unusual as the incorporation of selenium. While initially found in transfer and ribosomal RNAs, modifications also exist in messenger RNAs and noncoding RNAs. Modifications have profound cellular outcomes at various levels, such as altering RNA structure or being essential for cell survival or organism viability. The aberrant presence or absence of RNA modifications can lead to human disease, ranging from cancer to various metabolic and developmental illnesses such as Hoyeraal–Hreidarsson syndrome, Bowen–Conradi syndrome, or Williams–Beuren syndrome. In this review article, we summarize the characterization of all 143 currently known modified ribonucleosides by describing their taxonomic distributions, the enzymes that generate the modifications, and any implications in cellular processes, RNA structure, and disease. We also highlight areas of active research, such as specific RNAs that contain a particular type of modification as well as methodologies used to identify novel RNA modifications. This article is categorized under:RNA Processing > RNA Editing and Modification
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Affiliation(s)
- Phillip J McCown
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Agnieszka Ruszkowska
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Charlotte N Kunkler
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Kurtis Breger
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Jacob P Hulewicz
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Matthew C Wang
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Noah A Springer
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Jessica A Brown
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
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17
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Kim SC, Zhou L, Zhang W, O'Flaherty DK, Rondo-Brovetto V, Szostak JW. A Model for the Emergence of RNA from a Prebiotically Plausible Mixture of Ribonucleotides, Arabinonucleotides, and 2'-Deoxynucleotides. J Am Chem Soc 2020; 142:2317-2326. [PMID: 31913615 PMCID: PMC7577264 DOI: 10.1021/jacs.9b11239] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
The abiotic synthesis of ribonucleotides
is thought to have been
an essential step toward the emergence of the RNA world. However,
it is likely that the prebiotic synthesis of ribonucleotides was accompanied
by the simultaneous synthesis of arabinonucleotides, 2′-deoxyribonucleotides,
and other variations on the canonical nucleotides. In order to understand
how relatively homogeneous RNA could have emerged from such complex
mixtures, we have examined the properties of arabinonucleotides and
2′-deoxyribonucleotides in nonenzymatic template-directed primer
extension reactions. We show that nonenzymatic primer extension with
activated arabinonucleotides is much less efficient than with activated
ribonucleotides, and furthermore that once an arabinonucleotide is
incorporated, continued primer extension is strongly inhibited. As
previously shown, 2′-deoxyribonucleotides are also less efficiently
incorporated in primer extension reactions, but the difference is
more modest. Experiments with mixtures of nucleotides suggest that
the coexistence of ribo- and arabinonucleotides does not impede the
copying of RNA templates. Moreover, chimeric oligoribonucleotides
containing 2′-deoxy- or arabinonucleotides are effective templates
for RNA synthesis. We propose that the initial genetic polymers were
random sequence chimeric oligonucleotides formed by untemplated polymerization,
but that template copying chemistry favored RNA synthesis; multiple
rounds of replication may have led to pools of oligomers composed
mainly of RNA.
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Affiliation(s)
- Seohyun Chris Kim
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology , Massachusetts General Hospital , 185 Cambridge Street , Boston , Massachusetts 02114 , United States.,Department of Genetics , Harvard Medical School , 77 Avenue Louis Pasteur , Boston , Massachusetts 02115 , United States
| | - Lijun Zhou
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology , Massachusetts General Hospital , 185 Cambridge Street , Boston , Massachusetts 02114 , United States.,Department of Genetics , Harvard Medical School , 77 Avenue Louis Pasteur , Boston , Massachusetts 02115 , United States
| | - Wen Zhang
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology , Massachusetts General Hospital , 185 Cambridge Street , Boston , Massachusetts 02114 , United States.,Department of Genetics , Harvard Medical School , 77 Avenue Louis Pasteur , Boston , Massachusetts 02115 , United States
| | - Derek K O'Flaherty
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology , Massachusetts General Hospital , 185 Cambridge Street , Boston , Massachusetts 02114 , United States.,Department of Genetics , Harvard Medical School , 77 Avenue Louis Pasteur , Boston , Massachusetts 02115 , United States
| | - Valeria Rondo-Brovetto
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology , Massachusetts General Hospital , 185 Cambridge Street , Boston , Massachusetts 02114 , United States.,Department of Genetics , Harvard Medical School , 77 Avenue Louis Pasteur , Boston , Massachusetts 02115 , United States
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology , Massachusetts General Hospital , 185 Cambridge Street , Boston , Massachusetts 02114 , United States.,Department of Genetics , Harvard Medical School , 77 Avenue Louis Pasteur , Boston , Massachusetts 02115 , United States
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18
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Kumar R, Springsteen G, Krishnamurthy R. Synthesis of 2-Thioorotidine and Comparison of Its Unusual Instability with Its Canonical Pyrimidine Counterparts. J Org Chem 2019; 84:14427-14435. [PMID: 31608636 DOI: 10.1021/acs.joc.9b01546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
2-Thiopyrimidine nucleosides exhibit properties that are interesting from both a biological/medicinal and origins of life chemistry point of view. We report here the first synthesis of the nucleoside 2-thioorotidine and our observations on its unexpected lability with respect to its N-glycosidic bond when compared with its corresponding canonical pyrimidine counterparts. We hypothesize that the cause of the lability of the N-glycosidic bond is due to the combined steric and electronic effects from the 2-thio- and the 6-carboxyl groups, a lability that could, in turn, be useful for further chemical transformations.
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Affiliation(s)
- Ravi Kumar
- The Department of Chemistry , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States.,NSF/NASA Center for Chemical Evolution , Atlanta , Georgia 30332 , United States
| | - Greg Springsteen
- Department of Chemistry , Furman University , Greenville , South Carolina 29613 , United States.,NSF/NASA Center for Chemical Evolution , Atlanta , Georgia 30332 , United States
| | - Ramanarayanan Krishnamurthy
- The Department of Chemistry , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States.,NSF/NASA Center for Chemical Evolution , Atlanta , Georgia 30332 , United States
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19
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Computational and NMR studies of RNA duplexes with an internal pseudouridine-adenosine base pair. Sci Rep 2019; 9:16278. [PMID: 31700156 PMCID: PMC6838189 DOI: 10.1038/s41598-019-52637-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 10/03/2019] [Indexed: 01/28/2023] Open
Abstract
Pseudouridine (Ψ) is the most common chemical modification present in RNA. In general, Ψ increases the thermodynamic stability of RNA. However, the degree of stabilization depends on the sequence and structural context. To explain experimentally observed sequence dependence of the effect of Ψ on the thermodynamic stability of RNA duplexes, we investigated the structure, dynamics and hydration of RNA duplexes with an internal Ψ-A base pair in different nearest-neighbor sequence contexts. The structures of two RNA duplexes containing 5′-GΨC/3′-CAG and 5′-CΨG/3′-GAC motifs were determined using NMR spectroscopy. To gain insight into the effect of Ψ on duplex dynamics and hydration, we performed molecular dynamics (MD) simulations of RNA duplexes with 5′-GΨC/3′-CAG, 5′-CΨG/3′-GAC, 5′-AΨU/3′-UAA and 5′-UΨA/3′-AAU motifs and their unmodified counterparts. Our results showed a subtle impact from Ψ modification on the structure and dynamics of the RNA duplexes studied. The MD simulations confirmed the change in hydration pattern when U is replaced with Ψ. Quantum chemical calculations showed that the replacement of U with Ψ affected the intrinsic stacking energies at the base pair steps depending on the sequence context. The calculated intrinsic stacking energies help to explain the experimentally observed sequence dependent changes in the duplex stability from Ψ modification.
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20
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Alcolea Palafox M, Franklin Benial AM, K Rastogi V. Biomolecules of 2-Thiouracil, 4-Thiouracil and 2,4-Dithiouracil: A DFT Study of the Hydration, Molecular Docking and Effect in DNA:RNAMicrohelixes. Int J Mol Sci 2019; 20:E3477. [PMID: 31311161 PMCID: PMC6678171 DOI: 10.3390/ijms20143477] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/10/2019] [Accepted: 07/11/2019] [Indexed: 12/17/2022] Open
Abstract
The molecular structure of 2-thiouracil, 4-thiouracil and 2,4-dithiouracil was analyzed under the effect of the first and second hydration shell by using the B3LYP density functional (DFT) method, and the results were compared to those obtained for the uracil molecule. A slight difference in the water distribution appears in these molecules. On the hydration of these molecules several trends in bond lengths and atomic charges were established. The ring in uracil molecule appears easier to be deformed and adapted to different environments as compared to that when it is thio-substituted. Molecular docking calculations of 2-thiouracil against three different pathogens: Bacillus subtilis, Escherichia coli and Candida albicans were carried out. Docking calculations of 2,4-dithiouracil ligand with various targeted proteins were also performed. Different DNA: RNA hybrid microhelixes with uridine, 2-thiouridine, 4-thiouridine and 2,4-dithiouridine nucleosides were optimized in a simple model with three nucleotide base pairs. Two main types of microhelixes were analyzed in detail depending on the intramolecular H-bond of the 2'-OH group. The weaker Watson-Crick (WC) base pair formed with thio-substituted uracil than with unsubstituted ones slightly deforms the helical and backbone parameters, especially with 2,4-dithiouridine. However, the thio-substitution significantly increases the dipole moment of the A-type microhelixes, as well as the rise and propeller twist parameters.
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Affiliation(s)
- M Alcolea Palafox
- Departamento de Química-Física, Facultad de CienciasQuímicas, Universidad Complutense de Madrid, 28040 Madrid, Spain.
| | | | - V K Rastogi
- Indian Spectroscopy Society, KC 68/1, Old Kavinagar, Ghaziabad 201002, India
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21
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Xu J, Green NJ, Gibard C, Krishnamurthy R, Sutherland JD. Prebiotic phosphorylation of 2-thiouridine provides either nucleotides or DNA building blocks via photoreduction. Nat Chem 2019; 11:457-462. [PMID: 30936523 DOI: 10.1038/s41557-019-0225-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 01/25/2019] [Indexed: 11/09/2022]
Abstract
Breakthroughs in the study of the origin of life have demonstrated how some of the building blocks essential to biology could have been formed under various primordial scenarios, and could therefore have contributed to the chemical evolution of life. Missing building blocks are then sometimes inferred to be products of primitive biosynthesis, which can stretch the limits of plausibility. Here, we demonstrate the synthesis of 2'-deoxy-2-thiouridine, and subsequently 2'-deoxyadenosine and 2-deoxyribose, under prebiotic conditions. 2'-Deoxy-2-thiouridine is produced by photoreduction of 2,2'-anhydro-2-thiouridine, which is in turn formed by phosphorylation of 2-thiouridine-an intermediate of prebiotic RNA synthesis. 2'-Deoxy-2-thiouridine is an effective deoxyribosylating agent and may have functioned as such in either abiotic or proto-enzyme-catalysed pathways to DNA, as demonstrated by its conversion to 2'-deoxyadenosine by reaction with adenine, and 2-deoxyribose by hydrolysis. An alternative prebiotic phosphorylation of 2-thiouridine leads to the formation of its 5'-phosphate, showing that hypotheses in which 2-thiouridine was a key component of early RNA sequences are within the bounds of synthetic credibility.
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Affiliation(s)
- Jianfeng Xu
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | - Clémentine Gibard
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
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22
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Alcolea Palafox M. Effect of the sulfur atom on S2 and S4 positions of the uracil ring in different DNA:RNA hybrid microhelixes with three nucleotide base pairs. Biopolymers 2019; 110:e23247. [PMID: 30676643 DOI: 10.1002/bip.23247] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 11/03/2018] [Accepted: 11/07/2018] [Indexed: 02/06/2023]
Abstract
The effect of the sulphur atom on the uracil ring was analyzed in different DNA:RNA microhelixes with three nucleotide base-pairs, including uridine, 2-thiouridine, 4-thiouridine, 2,4-dithiouridine, cytidine, adenosine and guanosine. Distinct backbone and helical parameters were optimized at different density functional (DFT) levels. The Watson-Crick pair with 2-thiouridine appears weaker than with uridine, but its interaction with water molecules appears easier. Two types of microhelixes were found, depending on the H-bond of H2' hydroxyl atom: A-type appears with the ribose ring in 3 E-envelope C3' -endo, and B-type in 2 E-envelope C2' -endo. B-type is less common but it is more stable and with higher dipole-moment. The sulphur atoms significantly increase the dipole-moment of the microhelix, as well as the rise and propeller twist parameters. Simulations with four Na atoms H-bonded to the phosphate groups, and further hydration with explicit water molecules were carried out. A re-definition of the numerical value calculation of several base-pair and base-stacking parameters is suggested.
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Affiliation(s)
- Mauricio Alcolea Palafox
- Departamento de Química-Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid, Spain
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23
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Boopathi AA, Sampath S, Narasimhaswamy T. Isothermal and non-isothermal cold crystallization of tetrabenzofluorene (TBF) molecules. NEW J CHEM 2019. [DOI: 10.1039/c8nj06514d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Isothermal and non-isothermal cold crystallization of TBFC homologs is investigated by varying the alkyl chain length from C8 to C18 employing HOPM, DSC and powder XRD techniques.
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Affiliation(s)
- A. A. Boopathi
- Polymer Science & Technology Division
- Council of Scientific and Industrial Research (CSIR)-Central Leather Research Institute (CLRI)
- Chennai - 600020
- India
- Academy of Scientific and Innovative Research (AcSIR)
| | - Srinivasan Sampath
- Department of Materials Science
- School of Technology
- Central University of Tamil Nadu
- Thiruvarur - 610101
- India
| | - T. Narasimhaswamy
- Polymer Science & Technology Division
- Council of Scientific and Industrial Research (CSIR)-Central Leather Research Institute (CLRI)
- Chennai - 600020
- India
- Academy of Scientific and Innovative Research (AcSIR)
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24
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The emerging impact of tRNA modifications in the brain and nervous system. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:412-428. [PMID: 30529455 DOI: 10.1016/j.bbagrm.2018.11.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 11/21/2018] [Accepted: 11/23/2018] [Indexed: 01/19/2023]
Abstract
A remarkable number of neurodevelopmental disorders have been linked to defects in tRNA modifications. These discoveries place tRNA modifications in the spotlight as critical modulators of gene expression pathways that are required for proper organismal growth and development. Here, we discuss the emerging molecular and cellular functions of the diverse tRNA modifications linked to cognitive and neurological disorders. In particular, we describe how the structure and location of a tRNA modification influences tRNA folding, stability, and function. We then highlight how modifications in tRNA can impact multiple aspects of protein translation that are instrumental for maintaining proper cellular proteostasis. Importantly, we describe how perturbations in tRNA modification lead to a spectrum of deleterious biological outcomes that can disturb neurodevelopment and neurological function. Finally, we summarize the biological themes shared by the different tRNA modifications linked to cognitive disorders and offer insight into the future questions that remain to decipher the role of tRNA modifications. This article is part of a Special Issue entitled: mRNA modifications in gene expression control edited by Dr. Soller Matthias and Dr. Fray Rupert.
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25
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Inosine, but none of the 8-oxo-purines, is a plausible component of a primordial version of RNA. Proc Natl Acad Sci U S A 2018; 115:13318-13323. [PMID: 30509978 PMCID: PMC6310819 DOI: 10.1073/pnas.1814367115] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The RNA world hypothesis assumes the abiotic synthesis of nucleotides, as well as their participation in nonenzymatic RNA replication. Whereas prebiotic syntheses of the canonical purine nucleotides remain inefficient, a prebiotically plausible route to the 8-oxo-purines has been reported. Although these noncanonical purine nucleotides are known to engage in non-Watson–Crick pairing with their canonical purine counterparts, their behavior in nonenzymatic RNA copying has not been evaluated. Our study indicates that none of the 8-oxo-purines behaves as a suitable substrate for nonenzymatic RNA copying. However, inosine turns out to exhibit reasonable rates and fidelities in RNA copying reactions. We propose that inosine could have served as a surrogate for guanosine in the early emergence of life. The emergence of primordial RNA-based life would have required the abiotic synthesis of nucleotides, and their participation in nonenzymatic RNA replication. Although considerable progress has been made toward potentially prebiotic syntheses of the pyrimidine nucleotides (C and U) and their 2-thio variants, efficient routes to the canonical purine nucleotides (A and G) remain elusive. Reported syntheses are low yielding and generate a large number of undesired side products. Recently, a potentially prebiotic pathway to 8-oxo-adenosine and 8-oxo-inosine has been demonstrated, raising the question of the suitability of the 8-oxo-purines as substrates for prebiotic RNA replication. Here we show that the 8-oxo-purine nucleotides are poor substrates for nonenzymatic RNA primer extension, both as activated monomers and when present in the template strand; their presence at the end of a primer also strongly reduces the rate and fidelity of primer extension. To provide a proper comparison with 8-oxo-inosine, we also examined primer extension reactions with inosine, and found that inosine exhibits surprisingly rapid and accurate nonenzymatic RNA copying. We propose that inosine, which can be derived from adenosine by deamination, could have acted as a surrogate for G in the earliest stages of the emergence of life.
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26
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Jabgunde AM, Jaziri F, Bande O, Froeyen M, Abramov M, Nguyen H, Schepers G, Lescrinier E, Pinheiro VB, Pezo V, Marlière P, Herdewijn P. Methylated Nucleobases: Synthesis and Evaluation for Base Pairing In Vitro and In Vivo. Chemistry 2018; 24:12695-12707. [DOI: 10.1002/chem.201802304] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 06/07/2018] [Indexed: 12/29/2022]
Affiliation(s)
- Amit M. Jabgunde
- KU Leuven; Rega Institute; Medicinal Chemistry; Herestraat 49 box 1041 3000 Leuven Belgium
| | - Faten Jaziri
- Génomique Métabolique, Genoscope; Institut François Jacob; CEA; CNRS; Univ Evry, Université Paris-Saclay; 91057 Evry France
| | - Omprakash Bande
- KU Leuven; Rega Institute; Medicinal Chemistry; Herestraat 49 box 1041 3000 Leuven Belgium
| | - Matheus Froeyen
- KU Leuven; Rega Institute; Medicinal Chemistry; Herestraat 49 box 1041 3000 Leuven Belgium
| | - Mikhail Abramov
- KU Leuven; Rega Institute; Medicinal Chemistry; Herestraat 49 box 1041 3000 Leuven Belgium
| | - Hoai Nguyen
- KU Leuven; Rega Institute; Medicinal Chemistry; Herestraat 49 box 1041 3000 Leuven Belgium
| | - Guy Schepers
- KU Leuven; Rega Institute; Medicinal Chemistry; Herestraat 49 box 1041 3000 Leuven Belgium
| | - Eveline Lescrinier
- KU Leuven; Rega Institute; Medicinal Chemistry; Herestraat 49 box 1041 3000 Leuven Belgium
| | - Vitor B. Pinheiro
- Institute of Structural and Molecular Biology; University College London; Darwin Building, Gower Street London WC1E 6BT United Kingdom
| | - Valérie Pezo
- Génomique Métabolique, Genoscope; Institut François Jacob; CEA; CNRS; Univ Evry, Université Paris-Saclay; 91057 Evry France
| | - Philippe Marlière
- Génomique Métabolique, Genoscope; Institut François Jacob; CEA; CNRS; Univ Evry, Université Paris-Saclay; 91057 Evry France
| | - Piet Herdewijn
- KU Leuven; Rega Institute; Medicinal Chemistry; Herestraat 49 box 1041 3000 Leuven Belgium
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27
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Mlýnský V, Bussi G. Exploring RNA structure and dynamics through enhanced sampling simulations. Curr Opin Struct Biol 2018; 49:63-71. [PMID: 29414513 DOI: 10.1016/j.sbi.2018.01.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 12/20/2017] [Accepted: 01/02/2018] [Indexed: 01/23/2023]
Abstract
RNA function is intimately related to its structural dynamics. Molecular dynamics simulations are useful for exploring biomolecular flexibility but are severely limited by the accessible timescale. Enhanced sampling methods allow this timescale to be effectively extended in order to probe biologically relevant conformational changes and chemical reactions. Here, we review the role of enhanced sampling techniques in the study of RNA systems. We discuss the challenges and promises associated with the application of these methods to force-field validation, exploration of conformational landscapes and ion/ligand-RNA interactions, as well as catalytic pathways. Important technical aspects of these methods, such as the choice of the biased collective variables and the analysis of multi-replica simulations, are examined in detail. Finally, a perspective on the role of these methods in the characterization of RNA dynamics is provided.
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Affiliation(s)
- Vojtěch Mlýnský
- Scuola Internazionale Superiore di Studi Avanzati, SISSA, via Bonomea 265, 34136 Trieste, Italy
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati, SISSA, via Bonomea 265, 34136 Trieste, Italy.
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28
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Walton T, Szostak JW. A Kinetic Model of Nonenzymatic RNA Polymerization by Cytidine-5'-phosphoro-2-aminoimidazolide. Biochemistry 2017; 56:5739-5747. [PMID: 29022704 PMCID: PMC6340129 DOI: 10.1021/acs.biochem.7b00792] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The
nonenzymatic polymerization of RNA may have enabled copying
of functional sequences during the origin of life. Recent progress
utilizing 5′-phosphoro-2-aminoimidazole activation has reinvigorated
the possibility of using nonenzymatic RNA polymerization for copying
arbitrary sequences. However, the reasons why 2-aminoimidazole (AI)
is a superior activation group remain unclear. Here we report that
the predominant mechanism of polymerization using cytidine-5′-phosphoro-2-aminoimidazolide
(Cp*) involves a 2-aminoimidazolium-bridged dinucleotide (Cp*pC) intermediate.
To explore the role of this intermediate, we first identify and quantify
four reactions involving the synthesis and breakdown of Cp*pC that
occur in the absence of the primer–template duplex. We then
analyze the dependence of the rate of polymerization on the concentration
of the Cp*pC intermediate in the presence and absence of the competitive
inhibitor Cp. We also show that the contribution of the monomer Cp*
to the polymerization rate is negligible under our primer extension
conditions. Finally, we use the experimentally determined rate constants
of these reactions to develop a kinetic model that helps explain the
changing rate of nonenzymatic RNA polymerization over time. Our model
accounts for the concentration of Cp*pC formed by Cp* under primer
extension conditions. The model does not completely account for the
decline in polymerization rate observed over long times, which indicates
that additional important inhibitory processes have not yet been identified.
Our results suggest that the superiority of 2-aminoimidazole over
the traditional 2-methylimidazole activation is mostly due to the
higher level of accumulation of the imidazolium-bridged intermediate
under primer extension conditions.
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Affiliation(s)
- Travis Walton
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital , Boston, Massachusetts 02114, United States
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital , Boston, Massachusetts 02114, United States
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29
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Sochacka E, Lodyga-Chruscinska E, Pawlak J, Cypryk M, Bartos P, Ebenryter-Olbinska K, Leszczynska G, Nawrot B. C5-substituents of uridines and 2-thiouridines present at the wobble position of tRNA determine the formation of their keto-enol or zwitterionic forms - a factor important for accuracy of reading of guanosine at the 3΄-end of the mRNA codons. Nucleic Acids Res 2017; 45:4825-4836. [PMID: 28088758 PMCID: PMC5416851 DOI: 10.1093/nar/gkw1347] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 12/30/2016] [Indexed: 12/19/2022] Open
Abstract
Modified nucleosides present in the wobble position of the tRNA anticodons regulate protein translation through tuning the reading of mRNA codons. Among 40 of such nucleosides, there are modified uridines containing either a sulfur atom at the C2 position and/or a substituent at the C5 position of the nucleobase ring. It is already evidenced that tRNAs with 2-thiouridines at the wobble position preferentially read NNA codons, while the reading mode of the NNG codons by R5U/R5S2U-containing anticodons is still elusive. For a series of 18 modified uridines and 2-thiouridines, we determined the pKa values and demonstrated that both modifying elements alter the electron density of the uracil ring and modulate the acidity of their N3H proton. In aqueous solutions at physiological pH the 2-thiouridines containing aminoalkyl C5-substituents are ionized in ca. 50%. The results, confirmed also by theoretical calculations, indicate that the preferential binding of the modified units bearing non-ionizable 5-substituents to guanosine in the NNG codons may obey the alternative C-G-like (Watson–Crick) mode, while binding of those bearing aminoalkyl C5-substituents (protonated under physiological conditions) and especially those with a sulfur atom at the C2 position, adopt a zwitterionic form and interact with guanosine via a ‘new wobble’ pattern.
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Affiliation(s)
- Elzbieta Sochacka
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Elzbieta Lodyga-Chruscinska
- Institute of General Food Chemistry, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Justyna Pawlak
- Institute of General Food Chemistry, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Marek Cypryk
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Paulina Bartos
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Katarzyna Ebenryter-Olbinska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland.,Department of Computer Modeling, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Grazyna Leszczynska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Barbara Nawrot
- Department of Computer Modeling, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
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30
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Alcolea Palafox M, Rastogi V, Singh S. Effect of the sulphur atom on geometry and spectra of the biomolecule 2-thiouracil and in the WC base pair 2-thiouridine-adenosine. Influence of water in the first hydration shell. J Biomol Struct Dyn 2017; 36:1225-1254. [DOI: 10.1080/07391102.2017.1318304] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- M. Alcolea Palafox
- Facultad de Ciencias Químicas, Departamento de Química-Fisica1, Universidad Complutense, Madrid 28040, Spain
| | - V.K. Rastogi
- R.D. Foundation Group of Institutions, NH-58, Kadrabad, Modinagar, Ghaziabad, India
- Indian Spectroscopy Society, KC 68/1, Old Kavinagar, Ghaziabad 201 002, India
| | - S.P. Singh
- Department of Physics, Dr B R Ambedkar Govt Degree College, Mainpuri, India
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31
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Abstract
Wobble uridines (U34) are generally modified in all species. U34 modifications can be essential in metazoans but are not required for viability in fungi. In this review, we provide an overview on the types of modifications and how they affect the physico-chemical properties of wobble uridines. We describe the molecular machinery required to introduce these modifications into tRNA posttranscriptionally and discuss how posttranslational regulation may affect the activity of the modifying enzymes. We highlight the activity of anticodon specific RNases that target U34 containing tRNA. Finally, we discuss how defects in wobble uridine modifications lead to phenotypes in different species. Importantly, this review will mainly focus on the cytoplasmic tRNAs of eukaryotes. A recent review has extensively covered their bacterial and mitochondrial counterparts.1
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Affiliation(s)
- Raffael Schaffrath
- a Institut für Biologie, FG Mikrobiologie , Universität Kassel , Germany
| | - Sebastian A Leidel
- b Max Planck Institute for Molecular Biomedicine , Germany.,c Cells-in-Motion Cluster of Excellence , University of Münster , Münster , Germany.,d Medical Faculty , University of Münster , Albert-Schweitzer-Campus 1, Münster , Germany
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32
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Tam CP, Fahrenbach AC, Björkbom A, Prywes N, Izgu EC, Szostak JW. Downstream Oligonucleotides Strongly Enhance the Affinity of GMP to RNA Primer-Template Complexes. J Am Chem Soc 2017; 139:571-574. [PMID: 28055190 PMCID: PMC7547879 DOI: 10.1021/jacs.6b09760] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Indexed: 11/29/2022]
Abstract
Origins of life hypotheses often invoke a transitional phase of nonenzymatic template-directed RNA replication prior to the emergence of ribozyme-catalyzed copying of genetic information. Here, using NMR and ITC, we interrogate the binding affinity of guanosine 5'-monophosphate (GMP) for primer-template complexes when either another GMP, or a helper oligonucleotide, can bind downstream. Binding of GMP to a primer-template complex cannot be significantly enhanced by the possibility of downstream monomer binding, because the affinity of the downstream monomer is weaker than that of the first monomer. Strikingly, GMP binding affinity can be enhanced by ca. 2 orders of magnitude when a helper oligonucleotide is stably bound downstream of the monomer binding site. We compare these thermodynamic parameters to those previously reported for T7 RNA polymerase-mediated replication to help address questions of binding affinity in related nonenzymatic processes.
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Affiliation(s)
- Chun Pong Tam
- Howard
Hughes Medical Institute, Department of Molecular Biology and Center
for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford
Street, Cambridge, Massachusetts 02138, United States
| | - Albert C. Fahrenbach
- Howard
Hughes Medical Institute, Department of Molecular Biology and Center
for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Earth
Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Anders Björkbom
- Howard
Hughes Medical Institute, Department of Molecular Biology and Center
for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Department
of Biosciences, Åbo Akademi University, Åbo FI-20520, Finland
| | - Noam Prywes
- Howard
Hughes Medical Institute, Department of Molecular Biology and Center
for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford
Street, Cambridge, Massachusetts 02138, United States
| | - Enver Cagri Izgu
- Howard
Hughes Medical Institute, Department of Molecular Biology and Center
for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - Jack W. Szostak
- Howard
Hughes Medical Institute, Department of Molecular Biology and Center
for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford
Street, Cambridge, Massachusetts 02138, United States
- Earth
Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
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33
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Izgu EC, Oh SS, Szostak JW. Synthesis of activated 3'-amino-3'-deoxy-2-thio-thymidine, a superior substrate for the nonenzymatic copying of nucleic acid templates. Chem Commun (Camb) 2016; 52:3684-6. [PMID: 26857159 DOI: 10.1039/c5cc10317g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present a scalable synthesis of 3'-amino-3'-deoxy-2-thio-thymidine-5'-phosphoro-2-methylimidazolide, an activated monomer that can copy adenosine residues in nucleic acid templates rapidly without a polymerase. The sulfur atom substitution enhances the rate of template copying by 5-fold compared with the 3'-amino-3'-deoxy-T monomer, while the 3'-amino monomers exhibit a 2- to 30-fold enhancement compared with their ribonucleotide counterparts.
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Affiliation(s)
- Enver Cagri Izgu
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, USA. and Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
| | - Seung Soo Oh
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, USA. and Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, USA. and Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA and Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St., Cambridge, Massachusetts 02138, USA
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34
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Duechler M, Leszczyńska G, Sochacka E, Nawrot B. Nucleoside modifications in the regulation of gene expression: focus on tRNA. Cell Mol Life Sci 2016; 73:3075-95. [PMID: 27094388 PMCID: PMC4951516 DOI: 10.1007/s00018-016-2217-y] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 03/25/2016] [Accepted: 04/04/2016] [Indexed: 01/10/2023]
Abstract
Both, DNA and RNA nucleoside modifications contribute to the complex multi-level regulation of gene expression. Modified bases in tRNAs modulate protein translation rates in a highly dynamic manner. Synonymous codons, which differ by the third nucleoside in the triplet but code for the same amino acid, may be utilized at different rates according to codon-anticodon affinity. Nucleoside modifications in the tRNA anticodon loop can favor the interaction with selected codons by stabilizing specific base pairs. Similarly, weakening of base pairing can discriminate against binding to near-cognate codons. mRNAs enriched in favored codons are translated in higher rates constituting a fine-tuning mechanism for protein synthesis. This so-called codon bias establishes a basic protein level, but sometimes it is necessary to further adjust the production rate of a particular protein to actual requirements, brought by, e.g., stages in circadian rhythms, cell cycle progression or exposure to stress. Such an adjustment is realized by the dynamic change of tRNA modifications resulting in the preferential translation of mRNAs coding for example for stress proteins to facilitate cell survival. Furthermore, tRNAs contribute in an entirely different way to another, less specific stress response consisting in modification-dependent tRNA cleavage that contributes to the general down-regulation of protein synthesis. In this review, we summarize control functions of nucleoside modifications in gene regulation with a focus on recent findings on protein synthesis control by tRNA base modifications.
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Affiliation(s)
- Markus Duechler
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Lodz, Poland.
| | - Grażyna Leszczyńska
- Institute of Organic Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Lodz, Poland
| | - Elzbieta Sochacka
- Institute of Organic Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Lodz, Poland
| | - Barbara Nawrot
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Lodz, Poland
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35
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Structural effects of modified ribonucleotides and magnesium in transfer RNAs. Bioorg Med Chem 2016; 24:4826-4834. [PMID: 27364608 DOI: 10.1016/j.bmc.2016.06.037] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 06/16/2016] [Accepted: 06/17/2016] [Indexed: 11/20/2022]
Abstract
Modified nucleotides are ubiquitous and important to tRNA structure and function. To understand their effect on tRNA conformation, we performed a series of molecular dynamics simulations on yeast tRNAPhe and tRNAinit, Escherichia coli tRNAinit and HIV tRNALys. Simulations were performed with the wild type modified nucleotides, using the recently developed CHARMM compatible force field parameter set for modified nucleotides (J. Comput. Chem.2016, 37, 896), or with the corresponding unmodified nucleotides, and in the presence or absence of Mg2+. Results showed a stabilizing effect associated with the presence of the modifications and Mg2+ for some important positions, such as modified guanosine in position 37 and dihydrouridines in 16/17 including both structural properties and base interactions. Some other modifications were also found to make subtle contributions to the structural properties of local domains. While we were not able to investigate the effect of adenosine 37 in tRNAinit and limitations were observed in the conformation of E. coli tRNAinit, the presence of the modified nucleotides and of Mg2+ better maintained the structural features and base interactions of the tRNA systems than in their absence indicating the utility of incorporating the modified nucleotides in simulations of tRNA and other RNAs.
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36
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McKenney KM, Alfonzo JD. From Prebiotics to Probiotics: The Evolution and Functions of tRNA Modifications. Life (Basel) 2016; 6:E13. [PMID: 26985907 PMCID: PMC4810244 DOI: 10.3390/life6010013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 02/27/2016] [Accepted: 03/07/2016] [Indexed: 12/13/2022] Open
Abstract
All nucleic acids in cells are subject to post-transcriptional chemical modifications. These are catalyzed by a myriad of enzymes with exquisite specificity and that utilize an often-exotic array of chemical substrates. In no molecule are modifications more prevalent than in transfer RNAs. In the present document, we will attempt to take a chemical rollercoaster ride from prebiotic times to the present, with nucleoside modifications as key players and tRNA as the centerpiece that drove the evolution of biological systems to where we are today. These ideas will be put forth while touching on several examples of tRNA modification enzymes and their modus operandi in cells. In passing, we submit that the choice of tRNA is not a whimsical one but rather highlights its critical function as an essential invention for the evolution of protein enzymes.
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Affiliation(s)
- Katherine M McKenney
- The Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA.
| | - Juan D Alfonzo
- The Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA.
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.
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37
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Lee DK, Switzer C. Polymerase recognition of 2-thio-iso-guanine·5-methyl-4-pyrimidinone (iGs·P)--A new DD/AA base pair. Bioorg Med Chem Lett 2016; 26:1177-9. [PMID: 26821822 DOI: 10.1016/j.bmcl.2016.01.041] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 01/13/2016] [Accepted: 01/14/2016] [Indexed: 11/16/2022]
Abstract
Polymerase specificity is reported for a previously unknown base pair with a non-standard DD/AA hydrogen bonding pattern: 2-thio-iso-guanine·5-methyl-4-pyrimidinone. Our findings suggest that atomic substitution may provide a solution for low fidelity previously associated with enzymatic copying of iso-guanine.
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Affiliation(s)
- Dong-Kye Lee
- Department of Chemistry, University of California, Riverside, CA 92521, United States
| | - Christopher Switzer
- Department of Chemistry, University of California, Riverside, CA 92521, United States.
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