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Rathnayaka C, Chandrosoma IA, Choi J, Childers K, Chibuike M, Akabirov K, Shiri F, Hall AR, Lee M, McKinney C, Verber M, Park S, Soper SA. Detection and identification of single ribonucleotide monophosphates using a dual in-plane nanopore sensor made in a thermoplastic via replication. Lab Chip 2024; 24:2721-2735. [PMID: 38656267 DOI: 10.1039/d3lc01062g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
We report the generation of ∼8 nm dual in-plane pores fabricated in a thermoplastic via nanoimprint lithography (NIL). These pores were connected in series with nanochannels, one of which served as a flight tube to allow the identification of single molecules based on their molecular-dependent apparent mobilities (i.e., dual in-plane nanopore sensor). Two different thermoplastics were investigated including poly(methyl methacrylate), PMMA, and cyclic olefin polymer, COP, as the substrate for the sensor both of which were sealed using a low glass transition cover plate (cyclic olefin co-polymer, COC) that could be thermally fusion bonded to the PMMA or COP substrate at a temperature minimizing nanostructure deformation. Unique to these dual in-plane nanopore sensors was two pores flanking each side of the nanometer flight tube (50 × 50 nm, width × depth) that was 10 μm in length. The utility of this dual in-plane nanopore sensor was evaluated to not only detect, but also identify single ribonucleotide monophosphates (rNMPs) by using the travel time (time-of-flight, ToF), the resistive pulse event amplitude, and the dwell time. In spite of the relatively large size of these in-plane pores (∼8 nm effective diameter), we could detect via resistive pulse sensing (RPS) single rNMP molecules at a mass load of 3.9 fg, which was ascribed to the unique structural features of the nanofluidic network and the use of a thermoplastic with low relative dielectric constants, which resulted in a low RMS noise level in the open pore current. Our data indicated that the identification accuracy of individual rNMPs was high, which was ascribed to an improved chromatographic contribution to the nano-electrophoresis apparent mobility. With the ToF data only, the identification accuracy was 98.3%. However, when incorporating the resistive pulse sensing event amplitude and dwell time in conjunction with the ToF and analyzed via principal component analysis (PCA), the identification accuracy reached 100%. These findings pave the way for the realization of a novel chip-based single-molecule RNA sequencing technology.
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Affiliation(s)
- Chathurika Rathnayaka
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA.
- Center of BioModular Multiscale Systems for Precision Medicine, USA
| | - Indu A Chandrosoma
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA.
- Center of BioModular Multiscale Systems for Precision Medicine, USA
| | - Junseo Choi
- Center of BioModular Multiscale Systems for Precision Medicine, USA
- Mechanical & Industrial Engineering Department, Louisiana State University, Baton Rouge, LA 70803, USA.
| | - Katie Childers
- Center of BioModular Multiscale Systems for Precision Medicine, USA
- Bioengineering Program, The University of Kansas, Lawrence, KS 66045, USA
| | - Maximillian Chibuike
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA.
- Center of BioModular Multiscale Systems for Precision Medicine, USA
| | - Khurshed Akabirov
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA.
- Center of BioModular Multiscale Systems for Precision Medicine, USA
| | - Farhad Shiri
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA.
- Center of BioModular Multiscale Systems for Precision Medicine, USA
| | - Adam R Hall
- Center of BioModular Multiscale Systems for Precision Medicine, USA
- Virginia Tech-Wake Forest School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston Salem, NC 27101, USA
- Atrium Wake Forest Baptist Comprehensive Cancer Center, Wake Forest School of Medicine, Winston Salem, NC 27157, USA.
| | - Maxwell Lee
- Center of BioModular Multiscale Systems for Precision Medicine, USA
- Virginia Tech-Wake Forest School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston Salem, NC 27101, USA
| | - Collin McKinney
- Department of Chemistry, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA
| | - Matthew Verber
- Department of Chemistry, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA
| | - Sunggook Park
- Center of BioModular Multiscale Systems for Precision Medicine, USA
- Mechanical & Industrial Engineering Department, Louisiana State University, Baton Rouge, LA 70803, USA.
| | - Steven A Soper
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA.
- Center of BioModular Multiscale Systems for Precision Medicine, USA
- Department of Mechanical Engineering, The University of Kansas, Lawrence, KS 66045, USA
- Bioengineering Program, The University of Kansas, Lawrence, KS 66045, USA
- KU Cancer Center, University of Kansas Medical Center, Kansas City, KS 66160, USA
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2
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Pichon M, Levi-Acobas F, Kitoun C, Hollenstein M. 2',3'-Protected Nucleotides as Building Blocks for Enzymatic de novo RNA Synthesis. Chemistry 2024; 30:e202400137. [PMID: 38403849 DOI: 10.1002/chem.202400137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/13/2024] [Accepted: 02/20/2024] [Indexed: 02/27/2024]
Abstract
Besides being a key player in numerous fundamental biological processes, RNA also represents a versatile platform for the creation of therapeutic agents and efficient vaccines. The production of RNA oligonucleotides, especially those decorated with chemical modifications, cannot meet the exponential demand. Due to the inherent limits of solid-phase synthesis and in vitro transcription, alternative, biocatalytic approaches are in dire need to facilitate the production of RNA oligonucleotides. Here, we present a first step towards the controlled enzymatic synthesis of RNA oligonucleotides. We have explored the possibility of a simple protection step of the vicinal cis-diol moiety to temporarily block ribonucleotides. We demonstrate that pyrimidine nucleotides protected with acetals, particularly 2',3'-O-isopropylidene, are well-tolerated by the template-independent RNA polymerase PUP (polyU polymerase) and highly efficient coupling reactions can be achieved within minutes - an important feature for the development of enzymatic de novo synthesis protocols. Even though purines are not equally well-tolerated, these findings clearly demonstrate the possibility of using cis-diol-protected ribonucleotides combined with template-independent polymerases for the stepwise construction of RNA oligonucleotides.
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Affiliation(s)
- Maëva Pichon
- Institut Pasteur, Université Paris Cité, CNRS UMR3523, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
| | - Fabienne Levi-Acobas
- Institut Pasteur, Université Paris Cité, CNRS UMR3523, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
| | - Camélia Kitoun
- Institut Pasteur, Université Paris Cité, CNRS UMR3523, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
| | - Marcel Hollenstein
- Institut Pasteur, Université Paris Cité, CNRS UMR3523, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
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3
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Belfon KK, Sharma N, Zigweid R, Bolejack M, Davies D, Edwards TE, Myler PJ, French JB. Structure-Guided Discovery of N 5-CAIR Mutase Inhibitors. Biochemistry 2023; 62:2587-2596. [PMID: 37552766 PMCID: PMC10484210 DOI: 10.1021/acs.biochem.2c00705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 04/20/2023] [Indexed: 08/10/2023]
Abstract
Because purine nucleotides are essential for all life, differences between how microbes and humans metabolize purines can be exploited for the development of antimicrobial therapies. While humans biosynthesize purine nucleotides in a 10-step pathway, most microbes utilize an additional 11th enzymatic activity. The human enzyme, aminoimidazole ribonucleotide (AIR) carboxylase generates the product 4-carboxy-5-aminoimidazole ribonucleotide (CAIR) directly. Most microbes, however, require two separate enzymes, a synthetase (PurK) and a mutase (PurE), and proceed through the intermediate, N5-CAIR. Toward the development of therapeutics that target these differences, we have solved crystal structures of the N5-CAIR mutase of the human pathogens Legionella pneumophila (LpPurE) and Burkholderia cenocepacia (BcPurE) and used a structure-guided approach to identify inhibitors. Analysis of the structures reveals a highly conserved fold and active site architecture. Using this data, and three additional structures of PurE enzymes, we screened a library of FDA-approved compounds in silico and identified a set of 25 candidates for further analysis. Among these, we identified several new PurE inhibitors with micromolar IC50 values. Several of these compounds, including the α1-blocker Alfuzosin, inhibit the microbial PurE enzymes much more effectively than the human homologue. These structures and the newly described PurE inhibitors are valuable tools to aid in further studies of this enzyme and provide a foundation for the development of compounds that target differences between human and microbial purine metabolism.
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Affiliation(s)
- Kafi K.
J. Belfon
- Department
of Biochemistry and Cell Biology, Stony
Brook University, Stony
Brook, New York 11794, United States
| | - Nandini Sharma
- The
Hormel Institute, University of Minnesota, Austin, Minnesota 55912, United States
| | - Rachael Zigweid
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- Center
for Global Infectious Disease Research, Seattle Children’s Hospital, 307 Westlake Ave N Ste 500, Seattle, Washington 98109, United States
| | - Madison Bolejack
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
| | - Doug Davies
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- UCB-Bainbridge, Bainbridge Island, Washington 98110, United States
| | - Thomas E. Edwards
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- UCB-Bainbridge, Bainbridge Island, Washington 98110, United States
| | - Peter J. Myler
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- Center
for Global Infectious Disease Research, Seattle Children’s Hospital, 307 Westlake Ave N Ste 500, Seattle, Washington 98109, United States
- Department
of Global Health and Department of Biomedical Informatics and Medical
Education, University of Washington, Seattle, Washington 98195, United States
| | - Jarrod B. French
- The
Hormel Institute, University of Minnesota, Austin, Minnesota 55912, United States
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4
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Chinthapatla R, Sotoudegan M, Srivastava P, Anderson TK, Moustafa I, Passow K, Kennelly S, Moorthy R, Dulin D, Feng J, Harki D, Kirchdoerfer R, Cameron C, Arnold J. Interfering with nucleotide excision by the coronavirus 3'-to-5' exoribonuclease. Nucleic Acids Res 2023; 51:315-336. [PMID: 36546762 PMCID: PMC9841423 DOI: 10.1093/nar/gkac1177] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 11/11/2022] [Accepted: 11/27/2022] [Indexed: 12/24/2022] Open
Abstract
Some of the most efficacious antiviral therapeutics are ribonucleos(t)ide analogs. The presence of a 3'-to-5' proofreading exoribonuclease (ExoN) in coronaviruses diminishes the potency of many ribonucleotide analogs. The ability to interfere with ExoN activity will create new possibilities for control of SARS-CoV-2 infection. ExoN is formed by a 1:1 complex of nsp14 and nsp10 proteins. We have purified and characterized ExoN using a robust, quantitative system that reveals determinants of specificity and efficiency of hydrolysis. Double-stranded RNA is preferred over single-stranded RNA. Nucleotide excision is distributive, with only one or two nucleotides hydrolyzed in a single binding event. The composition of the terminal basepair modulates excision. A stalled SARS-CoV-2 replicase in complex with either correctly or incorrectly terminated products prevents excision, suggesting that a mispaired end is insufficient to displace the replicase. Finally, we have discovered several modifications to the 3'-RNA terminus that interfere with or block ExoN-catalyzed excision. While a 3'-OH facilitates hydrolysis of a nucleotide with a normal ribose configuration, this substituent is not required for a nucleotide with a planar ribose configuration such as that present in the antiviral nucleotide produced by viperin. Design of ExoN-resistant, antiviral ribonucleotides should be feasible.
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Affiliation(s)
- Rukesh Chinthapatla
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Mohamad Sotoudegan
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Pankaj Srivastava
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Thomas K Anderson
- Department of Biochemistry and Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ibrahim M Moustafa
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Kellan T Passow
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Samantha A Kennelly
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ramkumar Moorthy
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - David Dulin
- Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Junior Research Group 2, Interdisciplinary Center for Clinical Research, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Cauerstr. 3, 91058 Erlangen, Germany
| | - Joy Y Feng
- Gilead Sciences, Inc, Foster City, CA 94404, USA
| | - Daniel A Harki
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Robert N Kirchdoerfer
- Department of Biochemistry and Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Craig E Cameron
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Jamie J Arnold
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
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5
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Janissen R, Woodman A, Shengjuler D, Vallet T, Lee KM, Kuijpers L, Moustafa IM, Fitzgerald F, Huang PN, Perkins AL, Harki DA, Arnold JJ, Solano B, Shih SR, Vignuzzi M, Cameron CE, Dekker NH. Induced intra- and intermolecular template switching as a therapeutic mechanism against RNA viruses. Mol Cell 2021; 81:4467-4480.e7. [PMID: 34687604 PMCID: PMC8628313 DOI: 10.1016/j.molcel.2021.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/25/2021] [Accepted: 10/02/2021] [Indexed: 12/12/2022]
Abstract
Viral RNA-dependent RNA polymerases (RdRps) are a target for broad-spectrum antiviral therapeutic agents. Recently, we demonstrated that incorporation of the T-1106 triphosphate, a pyrazine-carboxamide ribonucleotide, into nascent RNA increases pausing and backtracking by the poliovirus RdRp. Here, by monitoring enterovirus A-71 RdRp dynamics during RNA synthesis using magnetic tweezers, we identify the "backtracked" state as an intermediate used by the RdRp for copy-back RNA synthesis and homologous recombination. Cell-based assays and RNA sequencing (RNA-seq) experiments further demonstrate that the pyrazine-carboxamide ribonucleotide stimulates these processes during infection. These results suggest that pyrazine-carboxamide ribonucleotides do not induce lethal mutagenesis or chain termination but function by promoting template switching and formation of defective viral genomes. We conclude that RdRp-catalyzed intra- and intermolecular template switching can be induced by pyrazine-carboxamide ribonucleotides, defining an additional mechanistic class of antiviral ribonucleotides with potential for broad-spectrum activity.
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Affiliation(s)
- Richard Janissen
- Department of Bionanoscience, Kavli Institute of Nanoscience, 2629 HZ Delft, the Netherlands
| | - Andrew Woodman
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College, PA 16801, USA
| | - Djoshkun Shengjuler
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Thomas Vallet
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Kuo-Ming Lee
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, 33302 Taoyuan, Taiwan
| | - Louis Kuijpers
- Department of Bionanoscience, Kavli Institute of Nanoscience, 2629 HZ Delft, the Netherlands
| | - Ibrahim M Moustafa
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College, PA 16801, USA
| | - Fiona Fitzgerald
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College, PA 16801, USA
| | - Peng-Nien Huang
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, 33302 Taoyuan, Taiwan
| | - Angela L Perkins
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Daniel A Harki
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA; Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jamie J Arnold
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College, PA 16801, USA
| | - Belén Solano
- Department of Bionanoscience, Kavli Institute of Nanoscience, 2629 HZ Delft, the Netherlands
| | - Shin-Ru Shih
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, 33302 Taoyuan, Taiwan
| | - Marco Vignuzzi
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Craig E Cameron
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College, PA 16801, USA.
| | - Nynke H Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, 2629 HZ Delft, the Netherlands.
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6
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Naydenova K, Muir KW, Wu LF, Zhang Z, Coscia F, Peet MJ, Castro-Hartmann P, Qian P, Sader K, Dent K, Kimanius D, Sutherland JD, Löwe J, Barford D, Russo CJ. Structure of the SARS-CoV-2 RNA-dependent RNA polymerase in the presence of favipiravir-RTP. Proc Natl Acad Sci U S A 2021; 118:e2021946118. [PMID: 33526596 PMCID: PMC7896311 DOI: 10.1073/pnas.2021946118] [Citation(s) in RCA: 121] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The RNA polymerase inhibitor favipiravir is currently in clinical trials as a treatment for infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), despite limited information about the molecular basis for its activity. Here we report the structure of favipiravir ribonucleoside triphosphate (favipiravir-RTP) in complex with the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) bound to a template:primer RNA duplex, determined by electron cryomicroscopy (cryoEM) to a resolution of 2.5 Å. The structure shows clear evidence for the inhibitor at the catalytic site of the enzyme, and resolves the conformation of key side chains and ions surrounding the binding pocket. Polymerase activity assays indicate that the inhibitor is weakly incorporated into the RNA primer strand, and suppresses RNA replication in the presence of natural nucleotides. The structure reveals an unusual, nonproductive binding mode of favipiravir-RTP at the catalytic site of SARS-CoV-2 RdRp, which explains its low rate of incorporation into the RNA primer strand. Together, these findings inform current and future efforts to develop polymerase inhibitors for SARS coronaviruses.
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Affiliation(s)
- Katerina Naydenova
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Kyle W Muir
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Long-Fei Wu
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Ziguo Zhang
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Francesca Coscia
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Mathew J Peet
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Pablo Castro-Hartmann
- Materials and Structural Analysis, Thermo Fisher Scientific, 5651 GG Eindhoven, The Netherlands
| | - Pu Qian
- Materials and Structural Analysis, Thermo Fisher Scientific, 5651 GG Eindhoven, The Netherlands
| | - Kasim Sader
- Materials and Structural Analysis, Thermo Fisher Scientific, 5651 GG Eindhoven, The Netherlands
| | - Kyle Dent
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Dari Kimanius
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - John D Sutherland
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom;
| | - Jan Löwe
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom;
| | - David Barford
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom;
| | - Christopher J Russo
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom;
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7
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Bernheim A, Millman A, Ofir G, Meitav G, Avraham C, Shomar H, Rosenberg MM, Tal N, Melamed S, Amitai G, Sorek R. Prokaryotic viperins produce diverse antiviral molecules. Nature 2021; 589:120-124. [PMID: 32937646 PMCID: PMC7610908 DOI: 10.1038/s41586-020-2762-2] [Citation(s) in RCA: 118] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 08/27/2020] [Indexed: 12/31/2022]
Abstract
Viperin is an interferon-induced cellular protein that is conserved in animals1. It has previously been shown to inhibit the replication of multiple viruses by producing the ribonucleotide 3'-deoxy-3',4'-didehydro (ddh)-cytidine triphosphate (ddhCTP), which acts as a chain terminator for viral RNA polymerase2. Here we show that eukaryotic viperin originated from a clade of bacterial and archaeal proteins that protect against phage infection. Prokaryotic viperins produce a set of modified ribonucleotides that include ddhCTP, ddh-guanosine triphosphate (ddhGTP) and ddh-uridine triphosphate (ddhUTP). We further show that prokaryotic viperins protect against T7 phage infection by inhibiting viral polymerase-dependent transcription, suggesting that it has an antiviral mechanism of action similar to that of animal viperin. Our results reveal a class of potential natural antiviral compounds produced by bacterial immune systems.
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Affiliation(s)
- Aude Bernheim
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Adi Millman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Gal Ofir
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Gilad Meitav
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Carmel Avraham
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | | | | | - Nir Tal
- Pantheon Biosciences, Yavne, Israel
| | - Sarah Melamed
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Gil Amitai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Rotem Sorek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
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8
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Zatopek KM, Alpaslan E, Evans T, Sauguet L, Gardner A. Novel ribonucleotide discrimination in the RNA polymerase-like two-barrel catalytic core of Family D DNA polymerases. Nucleic Acids Res 2020; 48:12204-12218. [PMID: 33137176 PMCID: PMC7708050 DOI: 10.1093/nar/gkaa986] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/08/2020] [Accepted: 10/12/2020] [Indexed: 02/06/2023] Open
Abstract
Family D DNA polymerase (PolD) is the essential replicative DNA polymerase for duplication of most archaeal genomes. PolD contains a unique two-barrel catalytic core absent from all other DNA polymerase families but found in RNA polymerases (RNAPs). While PolD has an ancestral RNA polymerase catalytic core, its active site has evolved the ability to discriminate against ribonucleotides. Until now, the mechanism evolved by PolD to prevent ribonucleotide incorporation was unknown. In all other DNA polymerase families, an active site steric gate residue prevents ribonucleotide incorporation. In this work, we identify two consensus active site acidic (a) and basic (b) motifs shared across the entire two-barrel nucleotide polymerase superfamily, and a nucleotide selectivity (s) motif specific to PolD versus RNAPs. A novel steric gate histidine residue (H931 in Thermococcus sp. 9°N PolD) in the PolD s-motif both prevents ribonucleotide incorporation and promotes efficient dNTP incorporation. Further, a PolD H931A steric gate mutant abolishes ribonucleotide discrimination and readily incorporates a variety of 2' modified nucleotides. Taken together, we construct the first putative nucleotide bound PolD active site model and provide structural and functional evidence for the emergence of DNA replication through the evolution of an ancestral RNAP two-barrel catalytic core.
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Affiliation(s)
| | - Ece Alpaslan
- New England Biolabs, 240 County Road Ipswich, MA 01938, USA
| | - Thomas C Evans
- New England Biolabs, 240 County Road Ipswich, MA 01938, USA
| | - Ludovic Sauguet
- Institut Pasteur, Unité de Dynamique Structurale des Macromolécules, 75015 Paris, France
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9
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Todd ZR, Fahrenbach AC, Ranjan S, Magnani CJ, Szostak JW, Sasselov DD. Ultraviolet-Driven Deamination of Cytidine Ribonucleotides Under Planetary Conditions. Astrobiology 2020; 20:878-888. [PMID: 32267736 PMCID: PMC9634989 DOI: 10.1089/ast.2019.2182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
A previously proposed synthesis of pyrimidine ribonucleotides makes use of ultraviolet (UV) light to convert β-d-ribocytidine-2',3'-cyclic phosphate to β-d-ribouridine-2',3'-cyclic phosphate, while simultaneously selectively degrading synthetic byproducts. Past studies of the photochemical reactions of pyrimidines have employed mercury arc lamps, characterized by narrowband emission centered at 254 nm, which is not representative of the UV environment of the early Earth. To further assess this process under more realistic circumstances, we investigated the wavelength dependence of the UV-driven conversion of β-d-ribocytidine-2',3'-cyclic phosphate to β-d-ribouridine-2',3'-cyclic phosphate. We used constraints provided by planetary environments to assess the implications for pyrimidine nucleotides on the early Earth. We found that the wavelengths of light (255-285 nm) that most efficiently drive the deamination of β-d-ribocytidine-2',3'-cyclic phosphate to β-d-ribouridine-2',3'-cyclic phosphate are accessible on planetary surfaces such as those of the Hadean-Archaean Earth for CO2-N2-dominated atmospheres. However, continued irradiation could eventually lead to low levels of ribocytidine in a low-temperature, highly irradiated environment, if production rates are slow.
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Affiliation(s)
- Zoe R. Todd
- Department of Astronomy, Harvard-Smithsonian Center for Astrophysics, Cambridge, Massachusetts
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts
- Address correspondence to: Zoe R. Todd, Department of Astronomy, Harvard-Smithsonian Center for Astrophysics, 60 Garden Street Mail-Stop 10, Cambridge, MA 02138
| | | | - Sukrit Ranjan
- SCOL Postdoctoral Fellow, Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Christopher J. Magnani
- Department of Astronomy, Harvard-Smithsonian Center for Astrophysics, Cambridge, Massachusetts
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts
| | - Jack W. Szostak
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts
| | - Dimitar D. Sasselov
- Department of Astronomy, Harvard-Smithsonian Center for Astrophysics, Cambridge, Massachusetts
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10
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Nava GM, Grasso L, Sertic S, Pellicioli A, Muzi Falconi M, Lazzaro F. One, No One, and One Hundred Thousand: The Many Forms of Ribonucleotides in DNA. Int J Mol Sci 2020; 21:E1706. [PMID: 32131532 PMCID: PMC7084774 DOI: 10.3390/ijms21051706] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 02/26/2020] [Accepted: 02/28/2020] [Indexed: 12/14/2022] Open
Abstract
In the last decade, it has become evident that RNA is frequently found in DNA. It is now well established that single embedded ribonucleoside monophosphates (rNMPs) are primarily introduced by DNA polymerases and that longer stretches of RNA can anneal to DNA, generating RNA:DNA hybrids. Among them, the most studied are R-loops, peculiar three-stranded nucleic acid structures formed upon the re-hybridization of a transcript to its template DNA. In addition, polyribonucleotide chains are synthesized to allow DNA replication priming, double-strand breaks repair, and may as well result from the direct incorporation of consecutive rNMPs by DNA polymerases. The bright side of RNA into DNA is that it contributes to regulating different physiological functions. The dark side, however, is that persistent RNA compromises genome integrity and genome stability. For these reasons, the characterization of all these structures has been under growing investigation. In this review, we discussed the origin of single and multiple ribonucleotides in the genome and in the DNA of organelles, focusing on situations where the aberrant processing of RNA:DNA hybrids may result in multiple rNMPs embedded in DNA. We concluded by providing an overview of the currently available strategies to study the presence of single and multiple ribonucleotides in DNA in vivo.
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Affiliation(s)
| | | | | | | | - Marco Muzi Falconi
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, 20133 Milano, Italy; (G.M.N.); (L.G.); (S.S.); (A.P.)
| | - Federico Lazzaro
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, 20133 Milano, Italy; (G.M.N.); (L.G.); (S.S.); (A.P.)
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11
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Motsch S, Tremmel P, Richert C. Regioselective formation of RNA strands in the absence of magnesium ions. Nucleic Acids Res 2020; 48:1097-1107. [PMID: 31819977 PMCID: PMC7026634 DOI: 10.1093/nar/gkz1125] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/08/2019] [Accepted: 11/18/2019] [Indexed: 11/28/2022] Open
Abstract
The oligomerization of ribonucleotides can produce short RNA strands in the absence of enzymes. This reaction gives one of two regioisomeric phosphodiester linkages, a 2',5'- or a 3',5'-diester. The former, non-natural linkage is detrimental for duplex stability, and is known to form preferentially in oligomerizations occurring in homogeneous solution with preactivated nucleotides in the presence of magnesium cations. We have studied ribonucleotide oligomerization with in situ activation, using NMR as monitoring technique. Unexpectedly, the known preference for 2',5'-linkages in the oligomerization of AMP was reversed in the absence of magnesium ions at slightly basic pH. Further, oligomerization was surprisingly efficient in the absence of Mg2+ salts, producing oligomers long enough for duplex formation. A quantitative systems chemistry analysis then revealed that the absence of magnesium ions favors the activation of nucleotides, and that the high concentration of active species can compensate for slower coupling. Further, organocatalytic intermediates can help to overcome the unfavorable regioselectivity of the magnesium-catalyzed reactions. Our findings allay concerns that RNA may have been difficult to form in the absence of enzymes. They also show that there is an efficient path to genetic material that does not require mineral surfaces or cations known to catalyze RNA hydrolysis.
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Affiliation(s)
- Sebastian Motsch
- Institute of Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Peter Tremmel
- Institute of Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Clemens Richert
- Institute of Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
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12
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Smith MR, Alnajjar KS, Hoitsma NM, Sweasy JB, Freudenthal BD. Molecular and structural characterization of oxidized ribonucleotide insertion into DNA by human DNA polymerase β. J Biol Chem 2020; 295:1613-1622. [PMID: 31892517 PMCID: PMC7008369 DOI: 10.1074/jbc.ra119.011569] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 12/29/2019] [Indexed: 01/07/2023] Open
Abstract
During oxidative stress, inflammation, or environmental exposure, ribo- and deoxyribonucleotides are oxidatively modified. 8-Oxo-7,8-dihydro-2'-guanosine (8-oxo-G) is a common oxidized nucleobase whose deoxyribonucleotide form, 8-oxo-dGTP, has been widely studied and demonstrated to be a mutagenic substrate for DNA polymerases. Guanine ribonucleotides are analogously oxidized to r8-oxo-GTP, which can constitute up to 5% of the rGTP pool. Because ribonucleotides are commonly misinserted into DNA, and 8-oxo-G causes replication errors, we were motivated to investigate how the oxidized ribonucleotide is utilized by DNA polymerases. To do this, here we employed human DNA polymerase β (pol β) and characterized r8-oxo-GTP insertion with DNA substrates containing either a templating cytosine (nonmutagenic) or adenine (mutagenic). Our results show that pol β has a diminished catalytic efficiency for r8-oxo-GTP compared with canonical deoxyribonucleotides but that r8-oxo-GTP is inserted mutagenically at a rate similar to those of other common DNA replication errors (i.e. ribonucleotide and mismatch insertions). Using FRET assays to monitor conformational changes of pol β with r8-oxo-GTP, we demonstrate impaired pol β closure that correlates with a reduced insertion efficiency. X-ray crystallographic analyses revealed that, similar to 8-oxo-dGTP, r8-oxo-GTP adopts an anti conformation opposite a templating cytosine and a syn conformation opposite adenine. However, unlike 8-oxo-dGTP, r8-oxo-GTP did not form a planar base pair with either templating base. These results suggest that r8-oxo-GTP is a potential mutagenic substrate for DNA polymerases and provide structural insights into how r8-oxo-GTP is processed by DNA polymerases.
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Affiliation(s)
- Mallory R Smith
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas 66160; Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas 66160
| | - Khadijeh S Alnajjar
- Department of Cellular and Molecular Medicine, University of Arizona Cancer Center, Tucson, Arizona 85724
| | - Nicole M Hoitsma
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas 66160; Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas 66160
| | - Joann B Sweasy
- Department of Cellular and Molecular Medicine, University of Arizona Cancer Center, Tucson, Arizona 85724
| | - Bret D Freudenthal
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas 66160; Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas 66160.
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13
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Kenderdine T, Nemati R, Baker A, Palmer M, Ujma J, FitzGibbon M, Deng L, Royzen M, Langridge J, Fabris D. High-resolution ion mobility spectrometry-mass spectrometry of isomeric/isobaric ribonucleotide variants. J Mass Spectrom 2020; 55:e4465. [PMID: 31697854 PMCID: PMC8363168 DOI: 10.1002/jms.4465] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/13/2019] [Accepted: 10/22/2019] [Indexed: 06/01/2023]
Abstract
In this report, we explored the benefits of cyclic ion mobility (cIM) mass spectrometry in the analysis of isomeric post-transcriptional modifications of RNA. Standard methyl-cytidine samples were initially utilized to test the ability to correctly distinguish different structures sharing the same elemental composition and thus molecular mass. Analyzed individually, the analytes displayed characteristic arrival times (tD ) determined by the different positions of the modifying methyl groups onto the common cytidine scaffold. Analyzed in mixture, the widths of the respective signals resulted in significant overlap that initially prevented their resolution on the tD scale. The separation of the four isomers was achieved by increasing the number of passes through the cIM device, which enabled to fully differentiate the characteristic ion mobility behaviors associated with very subtle structural variations. The placement of the cIM device between the mass-selective quadrupole and the time-of-flight analyzer allowed us to perform gas-phase activation of each of these ion populations, which had been first isolated according to a common mass-to-charge ratio and then separated on the basis of different ion mobility behaviors. The observed fragmentation patterns confirmed the structures of the various isomers thus substantiating the benefits of complementing unique tD information with specific fragmentation data to reach more stringent analyte identification. These capabilities were further tested by analyzing natural mono-nucleotide mixtures obtained by exonuclease digestion of total RNA extracts. In particular, the combination of cIM separation and post-mobility dissociation allowed us to establish the composition of methyl-cytidine and methyl-adenine components present in the entire transcriptome of HeLa cells. For this reason, we expect that this technique will benefit not only epitranscriptomic studies requiring the determination of identity and expression levels of RNA modifications, but also metabolomics investigations involving the analysis of natural extracts that may possibly contain subsets of isomeric/isobaric species.
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Affiliation(s)
| | | | - A. Baker
- Waters Corporation, Wilmslow SK9 4AX, UK
| | - M. Palmer
- Waters Corporation, Wilmslow SK9 4AX, UK
| | - J. Ujma
- Waters Corporation, Wilmslow SK9 4AX, UK
| | - M FitzGibbon
- University at Albany, Albany, NY 12222
- University of California San Diego, La Jolla, CA 92093
| | - L. Deng
- University at Albany, Albany, NY 12222
| | - M. Royzen
- University at Albany, Albany, NY 12222
| | | | - D. Fabris
- University at Albany, Albany, NY 12222
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14
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Sánchez-Salvador A, de Vega M. Structural Determinants Responsible for the Preferential Insertion of Ribonucleotides by Bacterial NHEJ PolDom. Biomolecules 2020; 10:biom10020203. [PMID: 32019147 PMCID: PMC7072297 DOI: 10.3390/biom10020203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 01/24/2020] [Accepted: 01/27/2020] [Indexed: 11/16/2022] Open
Abstract
The catalytic active site of the Polymerization Domain (PolDom) of bacterial Ligase D is designed to promote realignments of the primer and template strands and extend mispaired 3′ ends. These features, together with the preferred use of ribonucleotides (NTPs) over deoxynucleotides (dNTPs), allow PolDom to perform efficient double strand break repair by nonhomologous end joining when only a copy of the chromosome is present and the intracellular pool of dNTPs is depleted. Here, we evaluate (i) the role of conserved histidine and serine/threonine residues in NTP insertion, and (ii) the importance in the polymerization reaction of a conserved lysine residue that interacts with the templating nucleotide. To that extent, we have analyzed the biochemical properties of variants at the corresponding His651, Ser768, and Lys606 of Pseudomonas aeruginosa PolDom (Pa-PolDom). The results show that preferential insertion of NMPs is principally due to the histidine that also contributes to the plasticity of the active site to misinsert nucleotides. Additionally, Pa-PolDom Lys606 stabilizes primer dislocations. Finally, we show that the active site of PolDom allows the efficient use of 7,8-dihydro-8-oxo-riboguanosine triphosphate (8oxoGTP) as substrate, a major nucleotide lesion that results from oxidative stress, inserting with the same efficiency both the anti and syn conformations of 8oxoGMP.
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15
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Potapov V, Fu X, Dai N, Corrêa IR, Tanner NA, Ong JL. Base modifications affecting RNA polymerase and reverse transcriptase fidelity. Nucleic Acids Res 2019; 46:5753-5763. [PMID: 29750267 PMCID: PMC6009661 DOI: 10.1093/nar/gky341] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 04/18/2018] [Indexed: 01/28/2023] Open
Abstract
Ribonucleic acid (RNA) is capable of hosting a variety of chemically diverse modifications, in both naturally-occurring post-transcriptional modifications and artificial chemical modifications used to expand the functionality of RNA. However, few studies have addressed how base modifications affect RNA polymerase and reverse transcriptase activity and fidelity. Here, we describe the fidelity of RNA synthesis and reverse transcription of modified ribonucleotides using an assay based on Pacific Biosciences Single Molecule Real-Time sequencing. Several modified bases, including methylated (m6A, m5C and m5U), hydroxymethylated (hm5U) and isomeric bases (pseudouridine), were examined. By comparing each modified base to the equivalent unmodified RNA base, we can determine how the modification affected cumulative RNA polymerase and reverse transcriptase fidelity. 5-hydroxymethyluridine and N6-methyladenosine both increased the combined error rate of T7 RNA polymerase and reverse transcriptases, while pseudouridine specifically increased the error rate of RNA synthesis by T7 RNA polymerase. In addition, we examined the frequency, mutational spectrum and sequence context of reverse transcription errors on DNA templates from an analysis of second strand DNA synthesis.
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Affiliation(s)
| | - Xiaoqing Fu
- New England Biolabs, Inc, Ipswich, Massachusetts, 01938, USA
- Dalian University of Technology, School of Life Science and Biotechnology, Dalian, Liaoning 116021, China
| | - Nan Dai
- New England Biolabs, Inc, Ipswich, Massachusetts, 01938, USA
| | - Ivan R Corrêa
- New England Biolabs, Inc, Ipswich, Massachusetts, 01938, USA
| | - Nathan A Tanner
- New England Biolabs, Inc, Ipswich, Massachusetts, 01938, USA
| | - Jennifer L Ong
- New England Biolabs, Inc, Ipswich, Massachusetts, 01938, USA
- To whom correspondence should be addressed. Tel: +1 978 380 7448; Fax: +1 978 921 1350;
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16
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Liu Z, Ajram G, Rossi JC, Pascal R. The Chemical Likelihood of Ribonucleotide-α-Amino acid Copolymers as Players for Early Stages of Evolution. J Mol Evol 2019; 87:83-92. [PMID: 30788531 PMCID: PMC6443614 DOI: 10.1007/s00239-019-9887-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 01/17/2019] [Indexed: 11/25/2022]
Abstract
How ribosomal translation could have evolved remains an open question in most available scenarios for the early developments of life. Rather than considering RNA and peptides as two independent systems, this work is aimed at assessing the possibility of formation and stability of co-polymers or co-oligomers of α-amino acids and nucleotides from which translation might have evolved. Here we show that the linkages required to build such mixed structures have lifetimes of several weeks to months at neutral pH and 20 °C owing to the mutual protecting effect of both neighboring phosphoramidate and ester functional groups increasing their stability by factors of about 1 and 3 orders of magnitude, respectively. This protecting effect is reversible upon hydrolysis allowing the possibility of subsequent reactions. These copolymer models, for which an abiotic synthesis pathway is supported by experiments, form a basis from which both polymerization and translation could have logically evolved. Low temperatures were identified as a critical parameter for the kinetic stability of the aminoacylated nucleotide facilitating the synthesis of the model. This observation independently supports the views that any process involving RNA aminoacyl esters, outstandingly including the emergence of translation, was more probable at 0 °C or below and might be considered a kinetic marker constraining the environment in which translation has evolved.
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Affiliation(s)
- Ziwei Liu
- IBMM, University of Montpellier, CNRS, ENSCM, Montpellier, France
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
| | - Ghinwa Ajram
- IBMM, University of Montpellier, CNRS, ENSCM, Montpellier, France
| | | | - Robert Pascal
- IBMM, University of Montpellier, CNRS, ENSCM, Montpellier, France.
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17
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Srinivas V, Lebrette H, Lundin D, Kutin Y, Sahlin M, Lerche M, Eirich J, Branca RMM, Cox N, Sjöberg BM, Högbom M. Metal-free ribonucleotide reduction powered by a DOPA radical in Mycoplasma pathogens. Nature 2018; 563:416-420. [PMID: 30429545 PMCID: PMC6317698 DOI: 10.1038/s41586-018-0653-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 08/22/2018] [Indexed: 12/14/2022]
Abstract
Ribonucleotide reductase (RNR) catalyses the only known de novo pathway for the production of all four deoxyribonucleotides that are required for DNA synthesis1,2. It is essential for all organisms that use DNA as their genetic material and is a current drug target3,4. Since the discovery that iron is required for function in the aerobic, class I RNR found in all eukaryotes and many bacteria, a dinuclear metal site has been viewed as necessary to generate and stabilize the catalytic radical that is essential for RNR activity5-7. Here we describe a group of RNR proteins in Mollicutes-including Mycoplasma pathogens-that possess a metal-independent stable radical residing on a modified tyrosyl residue. Structural, biochemical and spectroscopic characterization reveal a stable 3,4-dihydroxyphenylalanine (DOPA) radical species that directly supports ribonucleotide reduction in vitro and in vivo. This observation overturns the presumed requirement for a dinuclear metal site in aerobic ribonucleotide reductase. The metal-independent radical requires new mechanisms for radical generation and stabilization, processes that are targeted by RNR inhibitors. It is possible that this RNR variant provides an advantage under metal starvation induced by the immune system. Organisms that encode this type of RNR-some of which are developing resistance to antibiotics-are involved in diseases of the respiratory, urinary and genital tracts. Further characterization of this RNR family and its mechanism of cofactor generation will provide insight into new enzymatic chemistry and be of value in devising strategies to combat the pathogens that utilize it. We propose that this RNR subclass is denoted class Ie.
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Affiliation(s)
- Vivek Srinivas
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
| | - Hugo Lebrette
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
| | - Daniel Lundin
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
| | - Yuri Kutin
- Max Planck Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Mülheim an der Ruhr, Germany
| | - Margareta Sahlin
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
| | - Michael Lerche
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
| | - Jürgen Eirich
- Cancer Proteomics Mass Spectrometry, Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Solna, Sweden
| | - Rui M M Branca
- Cancer Proteomics Mass Spectrometry, Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Solna, Sweden
| | - Nicholas Cox
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Britt-Marie Sjöberg
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden.
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
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18
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Pérez-Villa A, Saitta AM, Georgelin T, Lambert JF, Guyot F, Maurel MC, Pietrucci F. Synthesis of RNA Nucleotides in Plausible Prebiotic Conditions from ab Initio Computer Simulations. J Phys Chem Lett 2018; 9:4981-4987. [PMID: 30107125 DOI: 10.1021/acs.jpclett.8b02077] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Understanding the mechanism of spontaneous formation of ribonucleotides under realistic prebiotic conditions is a key open issue of origins-of-life research. In cells, de novo and salvage nucleotide enzymatic synthesis combines 5-phospho-α-d-ribose-1-diphosphate (α-PRPP) and nucleobases. Interestingly, these reactants are also known as prebiotically plausible compounds. Combining ab initio molecular dynamics simulations with recently developed reaction exploration and enhanced sampling methods, we show that nucleobases and α-PRPP should spontaneously combine, under mild hydrothermal conditions, with an exothermic reaction and a facile mechanism, forming both purine and pyrimidine ribonucleotides. Surprisingly, this mechanism is very similar to the biological one and yields ribonucleotides with the same anomeric carbon chirality as in biological systems. Mass spectrometry experiments performed on solutions of adenine and PRPP in similar conditions support the formation of AMP. These results suggest that natural selection might have optimized, through enzymes, a pre-existing ribonucleotide formation mechanism, carrying it forward to modern life forms.
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Affiliation(s)
- Andrea Pérez-Villa
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD, Institut de Minéralogie, de Physique des Matriaux et de Cosmochimie, IMPMC, F-75005 Paris , France
| | - A Marco Saitta
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD, Institut de Minéralogie, de Physique des Matriaux et de Cosmochimie, IMPMC, F-75005 Paris , France
| | - Thomas Georgelin
- Sorbonne Université, CNRS UMR 7197, Laboratoire de Réactivité de Surface, LRS, F-75005 Paris , France
- Centre de Biophysique Moléculaire, CNRS UPR 4301, F-45071 Orléans , France
| | - Jean-François Lambert
- Sorbonne Université, CNRS UMR 7197, Laboratoire de Réactivité de Surface, LRS, F-75005 Paris , France
| | - François Guyot
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD, Institut de Minéralogie, de Physique des Matriaux et de Cosmochimie, IMPMC, F-75005 Paris , France
| | - Marie-Christine Maurel
- Sorbonne Université, Muséum National d'Histoire Naturelle, CNRS MNHN UMR 7205, Institut de Systématique, Evolution, Biodiversité, ISyEB, F-75005 Paris , France
| | - Fabio Pietrucci
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD, Institut de Minéralogie, de Physique des Matriaux et de Cosmochimie, IMPMC, F-75005 Paris , France
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19
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Yarus M. Eighty routes to a ribonucleotide world; dispersion and stringency in the decisive selection. RNA 2018; 24:1041-1055. [PMID: 29785967 PMCID: PMC6049501 DOI: 10.1261/rna.066761.118] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 05/10/2018] [Indexed: 06/08/2023]
Abstract
We examine the initial emergence of genetics; that is, of an inherited chemical capability. The crucial actors are ribonucleotides, occasionally meeting in a prebiotic landscape. Previous work identified six influential variables during such random ribonucleotide pooling. Geochemical pools can be in periodic danger (e.g., from tides) or constant danger (e.g., from unfavorable weather). Such pools receive Gaussian nucleotide amounts sporadically, at random times, or get varying substrates simultaneously. Pools use cross-templated RNA synthesis (5'-5' product from 5'-3' template) or para-templated (5'-5' product from 5'-5' template) synthesis. Pools can undergo mild or strong selection, and be recently initiated (early) or late in age. Considering >80 combinations of these variables, selection calculations identify a superior route. Most likely, an early, sporadically fed, cross-templating pool in constant danger, receiving ≥1 mM nucleotides while under strong selection for a coenzyme-like product, will host selection of the first encoded biochemical functions. Predominantly templated products emerge from a critical event, the starting bloc selection, which exploits inevitable differences among early pools. Favorable selection has a simple rationale; it is increased by product dispersion (SD/mean), by selection intensity (mild or strong), or by combining these factors as stringency, reciprocal fraction of pools selected (1/sfsel). To summarize: chance utility, acting via a preference for disperse, templated coenzyme-like dinucleotides, uses stringent starting bloc selection to quickly establish majority encoded/genetic expression. Despite its computational origin, starting bloc selection is largely independent of specialized assumptions. This ribodinucleotide route to inheritance may also have facilitated 5'-3' chemical RNA replication.
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Affiliation(s)
- Michael Yarus
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, Colorado 80309-0347, USA
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Meroni A, Mentegari E, Crespan E, Muzi-Falconi M, Lazzaro F, Podestà A. The Incorporation of Ribonucleotides Induces Structural and Conformational Changes in DNA. Biophys J 2017; 113:1373-1382. [PMID: 28978432 PMCID: PMC5627062 DOI: 10.1016/j.bpj.2017.07.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 07/20/2017] [Accepted: 07/25/2017] [Indexed: 02/04/2023] Open
Abstract
Ribonucleotide incorporation is the most common error occurring during DNA replication. Cells have hence developed mechanisms to remove ribonucleotides from the genome and restore its integrity. Indeed, the persistence of ribonucleotides into DNA leads to severe consequences, such as genome instability and replication stress. Thus, it becomes important to understand the effects of ribonucleotides incorporation, starting from their impact on DNA structure and conformation. Here we present a systematic study of the effects of ribonucleotide incorporation into DNA molecules. We have developed, to our knowledge, a new method to efficiently synthesize long DNA molecules (hundreds of basepairs) containing ribonucleotides, which is based on a modified protocol for the polymerase chain reaction. By means of atomic force microscopy, we could therefore investigate the changes, upon ribonucleotide incorporation, of the structural and conformational properties of numerous DNA populations at the single-molecule level. Specifically, we characterized the scaling of the contour length with the number of basepairs and the scaling of the end-to-end distance with the curvilinear distance, the bending angle distribution, and the persistence length. Our results revealed that ribonucleotides affect DNA structure and conformation on scales that go well beyond the typical dimension of the single ribonucleotide. In particular, the presence of ribonucleotides induces a systematic shortening of the molecules, together with a decrease of the persistence length. Such structural changes are also likely to occur in vivo, where they could directly affect the downstream DNA transactions, as well as interfere with protein binding and recognition.
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Affiliation(s)
- Alice Meroni
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Elisa Mentegari
- DNA Enzymology and Molecular Virology, Institute of Molecular Genetics IGM-CNR, Pavia, Italy
| | - Emmanuele Crespan
- DNA Enzymology and Molecular Virology, Institute of Molecular Genetics IGM-CNR, Pavia, Italy
| | - Marco Muzi-Falconi
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy.
| | - Federico Lazzaro
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Alessandro Podestà
- Dipartimento di Fisica and C.I.Ma.I.Na, Università degli Studi di Milano, Milano, Italy.
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21
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Miao Z, Adamiak RW, Antczak M, Batey RT, Becka AJ, Biesiada M, Boniecki MJ, Bujnicki JM, Chen SJ, Cheng CY, Chou FC, Ferré-D'Amaré AR, Das R, Dawson WK, Ding F, Dokholyan NV, Dunin-Horkawicz S, Geniesse C, Kappel K, Kladwang W, Krokhotin A, Łach GE, Major F, Mann TH, Magnus M, Pachulska-Wieczorek K, Patel DJ, Piccirilli JA, Popenda M, Purzycka KJ, Ren A, Rice GM, Santalucia J, Sarzynska J, Szachniuk M, Tandon A, Trausch JJ, Tian S, Wang J, Weeks KM, Williams B, Xiao Y, Xu X, Zhang D, Zok T, Westhof E. RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme. RNA 2017; 23:655-672. [PMID: 28138060 PMCID: PMC5393176 DOI: 10.1261/rna.060368.116] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Accepted: 01/26/2017] [Indexed: 05/21/2023]
Abstract
RNA-Puzzles is a collective experiment in blind 3D RNA structure prediction. We report here a third round of RNA-Puzzles. Five puzzles, 4, 8, 12, 13, 14, all structures of riboswitch aptamers and puzzle 7, a ribozyme structure, are included in this round of the experiment. The riboswitch structures include biological binding sites for small molecules (S-adenosyl methionine, cyclic diadenosine monophosphate, 5-amino 4-imidazole carboxamide riboside 5'-triphosphate, glutamine) and proteins (YbxF), and one set describes large conformational changes between ligand-free and ligand-bound states. The Varkud satellite ribozyme is the most recently solved structure of a known large ribozyme. All puzzles have established biological functions and require structural understanding to appreciate their molecular mechanisms. Through the use of fast-track experimental data, including multidimensional chemical mapping, and accurate prediction of RNA secondary structure, a large portion of the contacts in 3D have been predicted correctly leading to similar topologies for the top ranking predictions. Template-based and homology-derived predictions could predict structures to particularly high accuracies. However, achieving biological insights from de novo prediction of RNA 3D structures still depends on the size and complexity of the RNA. Blind computational predictions of RNA structures already appear to provide useful structural information in many cases. Similar to the previous RNA-Puzzles Round II experiment, the prediction of non-Watson-Crick interactions and the observed high atomic clash scores reveal a notable need for an algorithm of improvement. All prediction models and assessment results are available at http://ahsoka.u-strasbg.fr/rnapuzzles/.
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Affiliation(s)
- Zhichao Miao
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de biologie moléculaire et cellulaire du CNRS, 67000 Strasbourg, France;
| | - Ryszard W Adamiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
- Poznan University of Technology, Institute of Computing Science, 60-965 Poznan, Poland
| | - Maciej Antczak
- Poznan University of Technology, Institute of Computing Science, 60-965 Poznan, Poland
| | - Robert T Batey
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309-0596, USA
| | - Alexander J Becka
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Marcin Biesiada
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Michał J Boniecki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland
- Laboratory of Bioinformatics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland
| | - Shi-Jie Chen
- Department of Physics and Astronomy, Department of Biochemistry, and Informatics Institute, University of Missouri-Columbia, Columbia, Missouri 65211, USA
| | - Clarence Yu Cheng
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Fang-Chieh Chou
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA
| | | | - Rhiju Das
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Wayne K Dawson
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, USA
| | - Nikolay V Dokholyan
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Stanisław Dunin-Horkawicz
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland
| | - Caleb Geniesse
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Kalli Kappel
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Wipapat Kladwang
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Andrey Krokhotin
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Grzegorz E Łach
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland
| | - François Major
- Institute for Research in Immunology and Cancer (IRIC), Department of Computer Science and Operations Research, Université de Montréal, Montréal, Québec, H3C 3J7, Canada
| | - Thomas H Mann
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Marcin Magnus
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland
| | | | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Joseph A Piccirilli
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA
| | - Mariusz Popenda
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Katarzyna J Purzycka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Aiming Ren
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Greggory M Rice
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, USA
| | - John Santalucia
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
- DNA Software, Ann Arbor, Michigan 48104, USA
| | - Joanna Sarzynska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Marta Szachniuk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
- Poznan University of Technology, Institute of Computing Science, 60-965 Poznan, Poland
| | - Arpit Tandon
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Jeremiah J Trausch
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309-0596, USA
| | - Siqi Tian
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Jian Wang
- Biomolecular Physics and Modeling Group, School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, USA
| | - Benfeard Williams
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Yi Xiao
- Biomolecular Physics and Modeling Group, School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Xiaojun Xu
- Department of Physics and Astronomy, Department of Biochemistry, and Informatics Institute, University of Missouri-Columbia, Columbia, Missouri 65211, USA
| | - Dong Zhang
- Department of Physics and Astronomy, Department of Biochemistry, and Informatics Institute, University of Missouri-Columbia, Columbia, Missouri 65211, USA
| | - Tomasz Zok
- Poznan University of Technology, Institute of Computing Science, 60-965 Poznan, Poland
| | - Eric Westhof
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de biologie moléculaire et cellulaire du CNRS, 67000 Strasbourg, France;
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22
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Siegel D, Hui HC, Doerffler E, Clarke MO, Chun K, Zhang L, Neville S, Carra E, Lew W, Ross B, Wang Q, Wolfe L, Jordan R, Soloveva V, Knox J, Perry J, Perron M, Stray KM, Barauskas O, Feng JY, Xu Y, Lee G, Rheingold AL, Ray AS, Bannister R, Strickley R, Swaminathan S, Lee WA, Bavari S, Cihlar T, Lo MK, Warren TK, Mackman RL. Discovery and Synthesis of a Phosphoramidate Prodrug of a Pyrrolo[2,1-f][triazin-4-amino] Adenine C-Nucleoside (GS-5734) for the Treatment of Ebola and Emerging Viruses. J Med Chem 2017; 60:1648-1661. [PMID: 28124907 PMCID: PMC7202039 DOI: 10.1021/acs.jmedchem.6b01594] [Citation(s) in RCA: 441] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Indexed: 12/12/2022]
Abstract
The recent Ebola virus (EBOV) outbreak in West Africa was the largest recorded in history with over 28,000 cases, resulting in >11,000 deaths including >500 healthcare workers. A focused screening and lead optimization effort identified 4b (GS-5734) with anti-EBOV EC50 = 86 nM in macrophages as the clinical candidate. Structure activity relationships established that the 1'-CN group and C-linked nucleobase were critical for optimal anti-EBOV potency and selectivity against host polymerases. A robust diastereoselective synthesis provided sufficient quantities of 4b to enable preclinical efficacy in a non-human-primate EBOV challenge model. Once-daily 10 mg/kg iv treatment on days 3-14 postinfection had a significant effect on viremia and mortality, resulting in 100% survival of infected treated animals [ Nature 2016 , 531 , 381 - 385 ]. A phase 2 study (PREVAIL IV) is currently enrolling and will evaluate the effect of 4b on viral shedding from sanctuary sites in EBOV survivors.
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Affiliation(s)
- Dustin Siegel
- Gilead
Sciences, Inc., Foster
City, California 94404, United States
| | - Hon C. Hui
- Gilead
Sciences, Inc., Foster
City, California 94404, United States
| | - Edward Doerffler
- Gilead
Sciences, Inc., Foster
City, California 94404, United States
| | | | - Kwon Chun
- Gilead
Sciences, Inc., Foster
City, California 94404, United States
| | - Lijun Zhang
- Gilead
Sciences, Inc., Foster
City, California 94404, United States
| | - Sean Neville
- Gilead
Sciences, Inc., Foster
City, California 94404, United States
| | - Ernest Carra
- Gilead
Sciences, Inc., Foster
City, California 94404, United States
| | - Willard Lew
- Gilead
Sciences, Inc., Foster
City, California 94404, United States
| | - Bruce Ross
- Gilead
Sciences, Inc., Foster
City, California 94404, United States
| | - Queenie Wang
- Gilead
Sciences, Inc., Foster
City, California 94404, United States
| | - Lydia Wolfe
- Gilead
Sciences, Inc., Foster
City, California 94404, United States
| | - Robert Jordan
- Gilead
Sciences, Inc., Foster
City, California 94404, United States
| | - Veronica Soloveva
- United
States Army Medical Research Institute of Infectious Diseases (USAMRIID), Frederick, Maryland 21702, United States
| | - John Knox
- Gilead
Sciences, Inc., Foster
City, California 94404, United States
| | - Jason Perry
- Gilead
Sciences, Inc., Foster
City, California 94404, United States
| | - Michel Perron
- Gilead
Sciences, Inc., Foster
City, California 94404, United States
| | - Kirsten M. Stray
- Gilead
Sciences, Inc., Foster
City, California 94404, United States
| | - Ona Barauskas
- Gilead
Sciences, Inc., Foster
City, California 94404, United States
| | - Joy Y. Feng
- Gilead
Sciences, Inc., Foster
City, California 94404, United States
| | - Yili Xu
- Gilead
Sciences, Inc., Foster
City, California 94404, United States
| | - Gary Lee
- Gilead
Sciences, Inc., Foster
City, California 94404, United States
| | - Arnold L. Rheingold
- University
of California—San Diego, San Diego, California 92093, United States
| | - Adrian S. Ray
- Gilead
Sciences, Inc., Foster
City, California 94404, United States
| | - Roy Bannister
- Gilead
Sciences, Inc., Foster
City, California 94404, United States
| | - Robert Strickley
- Gilead
Sciences, Inc., Foster
City, California 94404, United States
| | | | - William A. Lee
- Gilead
Sciences, Inc., Foster
City, California 94404, United States
| | - Sina Bavari
- United
States Army Medical Research Institute of Infectious Diseases (USAMRIID), Frederick, Maryland 21702, United States
| | - Tomas Cihlar
- Gilead
Sciences, Inc., Foster
City, California 94404, United States
| | - Michael K. Lo
- Centers
for Disease Control and Prevention, Atlanta, Georgia 30333, United States
| | - Travis K. Warren
- United
States Army Medical Research Institute of Infectious Diseases (USAMRIID), Frederick, Maryland 21702, United States
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23
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Zakataeva NP, Romanenkov DV, Yusupova YR, Skripnikova VS, Asahara T, Gronskiy SV. Identification, Heterologous Expression, and Functional Characterization of Bacillus subtilis YutF, a HAD Superfamily 5'-Nucleotidase with Broad Substrate Specificity. PLoS One 2016; 11:e0167580. [PMID: 27907199 PMCID: PMC5132288 DOI: 10.1371/journal.pone.0167580] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 11/16/2016] [Indexed: 11/25/2022] Open
Abstract
5'-nucleotidases (EC 3.1.3.5) catalyze the hydrolytic dephosphorylation of 5'-ribonucleotides and 5'-deoxyribonucleotides as well as complex nucleotides, such as uridine 5'-diphosphoglucose (UDP-glucose), nicotinamide adenine dinucleotide and flavin adenine dinucleotide, to their corresponding nucleosides plus phosphate. These enzymes have been found in diverse species in intracellular and membrane-bound, surface-localized forms. Soluble forms of 5'-nucleotidases belong to the ubiquitous haloacid dehalogenase superfamily (HADSF) and have been shown to be involved in the regulation of nucleotide, nucleoside and nicotinamide adenine dinucleotide (NAD+) pools. Despite the important role of 5'-nucleotidases in cellular metabolism, only a few of these enzymes have been characterized in the Gram-positive bacterium Bacillus subtilis, the workhorse industrial microorganism included in the Food and Drug Administration’s GRAS (generally regarded as safe) list. In the present study, we report the identification of a novel 5'-nucleotidase gene from B. subtilis, yutF, which comprises 771 bp encoding a 256-amino-acid protein belonging to the IIA subfamily of the HADSF. The gene product is responsible for the major p-nitrophenyl phosphatase activity in B. subtilis. The yutF gene was overexpressed in Escherichia coli, and its product fused to a polyhistidine tag was purified and biochemically characterized as a soluble 5'-nucleotidase with broad substrate specificity. The recombinant YutF protein was found to hydrolyze various purine and pyrimidine 5'-nucleotides, showing preference for 5'-nucleoside monophosphates and, specifically, 5'-XMP. Recombinant YutF also exhibited phosphohydrolase activity toward nucleotide precursors, ribose-5-phosphate and 5-phosphoribosyl-1-pyrophosphate. Determination of the kinetic parameters of the enzyme revealed a low substrate specificity (Km values in the mM concentration range) and modest catalytic efficiencies with respect to substrates. An initial study of the regulation of yutF expression showed that the yutF gene is a component of the yutDEF transcription unit and that YutF overproduction positively influences yutDEF expression.
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Affiliation(s)
| | | | | | | | - Takayuki Asahara
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc, Kawasaki, Kanagawa, Japan
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24
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Qi HH, Bao J, Zhang Q, Ma B, Gu GY, Zhang PL, Ou-Yang G, Wu ZM, Ying HJ, Ou-Yang PK. Wnt/β-catenin signaling plays an important role in the protective effects of FDP-Sr against oxidative stress induced apoptosis in MC3T3-E1 cell. Bioorg Med Chem Lett 2016; 26:4720-4723. [PMID: 27575480 DOI: 10.1016/j.bmcl.2016.08.043] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Revised: 07/25/2016] [Accepted: 08/17/2016] [Indexed: 11/19/2022]
Abstract
Strontium fructose 1,6-diphosphate (FDP-Sr) is a new strontium-containing compound. The primary aim of this study was to clarify whether the structure component of FDP-Sr, FDP could benefit the protective effect of Sr (II) against oxidative stress induced apoptosis, and meanwhile to further explore the important role of Wnt/β-catenin signaling in the anti-apoptosis effect of FDP-Sr in response to oxidative stress induced by H2O2 in an osteoblastic MC3T3-E1 cell line. Results showed that FDP-Sr could improve the osteoblastic differentiation under oxidative stress with induced cell proliferation and improved mineralization. The inhibition effect of FDP-Sr on cell apoptosis induced by H2O2 was proved by reduced reactive oxygen species production and activated caspase3. Under oxidative stress, mRNA and protein levels of phospho-β-catenin reduced, while β-catenin increased in the FDP-Sr treatment cell, leaded to the up-regulations of Runx2 and OPG at both mRNA and protein levels, finally improved the differentiation of osteoblasts. By the engagement of Wnt/β-catenin pathway's inhibitor (XAV-939), the protective effects of FDP-Sr on osteoblastic differentiation against oxidative stress were repressed along with inhibited wnt/β-catenin signaling and reduced mRNA and protein levels of Runx2 and OPG. In conclusion, FDP-Sr was demonstrated to protect osteoblast differentiation from oxidative damage induced by H2O2 through up-regulation of Wnt/β-catenin signaling, and FDP in FDP-Sr was able to directly improve the oxidative stress injury through its ROS scavenging ability.
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Affiliation(s)
- Huan-Huan Qi
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing 210009, People's Republic of China
| | - Jun Bao
- Jiangsu Province of Ficial Hospital, Nanjing 210024, People's Republic of China
| | - Qi Zhang
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing 210009, People's Republic of China.
| | - Bo Ma
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing 210009, People's Republic of China.
| | - Gui-Ying Gu
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing 210009, People's Republic of China
| | - Peng-Ling Zhang
- Jiangsu Province of Ficial Hospital, Nanjing 210024, People's Republic of China
| | - Gang Ou-Yang
- Jiangsu Province of Ficial Hospital, Nanjing 210024, People's Republic of China
| | - Zi-Mei Wu
- School of Pharmacy, FMHS, The University of Auckland Private Bag 92019, Auckland 1142, New Zealand
| | - Han-Jie Ying
- School of Life Science & Pharmaceutical Engineering, Nanjing Tech University, Nanjing 210009, People's Republic of China
| | - Ping-Kai Ou-Yang
- School of Life Science & Pharmaceutical Engineering, Nanjing Tech University, Nanjing 210009, People's Republic of China
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25
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Oka M, Takegawa K, Kimura Y. Lysyl-tRNA synthetase from Myxococcus xanthus catalyzes the formation of diadenosine penta- and hexaphosphates from adenosine tetraphosphate. Arch Biochem Biophys 2016; 604:152-8. [PMID: 27392456 DOI: 10.1016/j.abb.2016.07.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 06/23/2016] [Accepted: 07/02/2016] [Indexed: 11/18/2022]
Abstract
Myxococcus xanthus lysyl-tRNA synthetase (LysS) produces diadenosine tetraphosphate (Ap4A) from ATP in the presence of Mn(2+); in the present study, it also generated Ap4 from ATP and triphosphate. When ATP and Ap4 were incubated with LysS and pyrophosphatase, first Ap4A, Ap5A, and ADP, and then Ap5, Ap6A, and Ap3A were generated. The results suggest that in the first step, LysS can form lysyl-AMP and lysyl-ADP intermediates from Ap4 and release triphosphate and diphosphate, respectively, whereas in the second step, it can produce Ap5 from lysyl-ADP with triphosphate, and Ap6A from lysyl-ADP with Ap4. In addition, in the presence of Ap4 and pyrophosphatase, but absence of ATP, LysS also generates diadenosine oligophosphates (ApnAs: n = 3-6). These results indicate that LysS has the ability to catalyze the formation of various ApnAs from Ap4 in the presence of pyrophosphatase. Furthermore, the formation of Ap4A by LysS was inhibited by tRNA(Lys) in the presence of 1 mM ATP. To the best of our knowledge, this is the first report of Ap5A and Ap6A synthesis by lysyl-tRNA synthetase.
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Affiliation(s)
- Manami Oka
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, Miki-cho, Kagawa, Japan
| | - Kaoru Takegawa
- Department of Bioscience and Biotechnology, Kyusyu University, Hakozaki, Higashi-ku, Fukuoka, Japan
| | - Yoshio Kimura
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, Miki-cho, Kagawa, Japan.
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26
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Abstract
G(5')pp(5')G synthesis from pG and chemically activated 2MeImpG is accelerated by the addition of complementary poly(C), but affected only slightly by poly(G) and not at all by poly(U) and poly(A). This suggests that 3'-5' poly(C) is a template for uncatalyzed synthesis of 5'-5' GppG, as was poly(U) for AppA synthesis, previously. The reaction occurs at 50 mM mono- and divalent ion concentrations, at moderate temperatures, and near pH 7. The reactive complex at the site of enhanced synthesis of 5'-5' GppG seems to contain a single pG, a single phosphate-activated nucleotide 2 MeImpG, and a single strand of poly(C). Most likely this structure is base-paired, as the poly(C)-enhanced reaction is completely disrupted between 30 and 37 °C, whereas slower, untemplated synthesis of GppG accelerates. More specifically, the reactive center acts as would be expected for short, isolated G nucleotide stacks expanded and ordered by added poly(C). For example, poly(C)-mediated GppG production is very nonlinear in overall nucleotide concentration. Uncatalyzed NppN synthesis is now known for two polymers and their complementary free nucleotides. These data suggest that varied, simple, primordial 3'-5' RNA sequences could express a specific chemical phenotype by encoding synthesis of complementary, reactive, coenzyme-like 5'-5' ribodinucleotides.
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Affiliation(s)
- Irene Majerfeld
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado 80309-0347, USA
| | - Deepa Puthenvedu
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado 80309-0347, USA
| | - Michael Yarus
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado 80309-0347, USA
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27
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Cilli P, Minoprio A, Bossa C, Bignami M, Mazzei F. Formation and Repair of Mismatches Containing Ribonucleotides and Oxidized Bases at Repeated DNA Sequences. J Biol Chem 2015; 290:26259-69. [PMID: 26338705 PMCID: PMC4646274 DOI: 10.1074/jbc.m115.679209] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 09/02/2015] [Indexed: 11/06/2022] Open
Abstract
The cellular pool of ribonucleotide triphosphates (rNTPs) is higher than that of deoxyribonucleotide triphosphates. To ensure genome stability, DNA polymerases must discriminate against rNTPs and incorporated ribonucleotides must be removed by ribonucleotide excision repair (RER). We investigated DNA polymerase β (POL β) capacity to incorporate ribonucleotides into trinucleotide repeated DNA sequences and the efficiency of base excision repair (BER) and RER enzymes (OGG1, MUTYH, and RNase H2) when presented with an incorrect sugar and an oxidized base. POL β incorporated rAMP and rCMP opposite 7,8-dihydro-8-oxoguanine (8-oxodG) and extended both mispairs. In addition, POL β was able to insert and elongate an oxidized rGMP when paired with dA. We show that RNase H2 always preserves the capacity to remove a single ribonucleotide when paired to an oxidized base or to incise an oxidized ribonucleotide in a DNA duplex. In contrast, BER activity is affected by the presence of a ribonucleotide opposite an 8-oxodG. In particular, MUTYH activity on 8-oxodG:rA mispairs is fully inhibited, although its binding capacity is retained. This results in the reduction of RNase H2 incision capability of this substrate. Thus complex mispairs formed by an oxidized base and a ribonucleotide can compromise BER and RER in repeated sequences.
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Affiliation(s)
- Piera Cilli
- From the Department of Environment and Primary Prevention, Istituto Superiore di Sanità, 00161 Roma and the Department of Science, University Roma Tre, 00154 Roma, Italy
| | - Anna Minoprio
- From the Department of Environment and Primary Prevention, Istituto Superiore di Sanità, 00161 Roma and
| | - Cecilia Bossa
- From the Department of Environment and Primary Prevention, Istituto Superiore di Sanità, 00161 Roma and
| | - Margherita Bignami
- From the Department of Environment and Primary Prevention, Istituto Superiore di Sanità, 00161 Roma and
| | - Filomena Mazzei
- From the Department of Environment and Primary Prevention, Istituto Superiore di Sanità, 00161 Roma and
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Burcar BT, Barge LM, Trail D, Watson EB, Russell MJ, McGown LB. RNA Oligomerization in Laboratory Analogues of Alkaline Hydrothermal Vent Systems. Astrobiology 2015; 15:509-522. [PMID: 26154881 DOI: 10.1089/ast.2014.1280] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Discovering pathways leading to long-chain RNA formation under feasible prebiotic conditions is an essential step toward demonstrating the viability of the RNA World hypothesis. Intensive research efforts have provided evidence of RNA oligomerization by using circular ribonucleotides, imidazole-activated ribonucleotides with montmorillonite catalyst, and ribonucleotides in the presence of lipids. Additionally, mineral surfaces such as borates, apatite, and calcite have been shown to catalyze the formation of small organic compounds from inorganic precursors (Cleaves, 2008 ), pointing to possible geological sites for the origins of life. Indeed, the catalytic properties of these particular minerals provide compelling evidence for alkaline hydrothermal vents as a potential site for the origins of life since, at these vents, large metal-rich chimney structures can form that have been shown to be energetically favorable to diverse forms of life. Here, we test the ability of iron- and sulfur-rich chimneys to support RNA oligomerization reactions using imidazole-activated and non-activated ribonucleotides. The chimneys were synthesized in the laboratory in aqueous "ocean" solutions under conditions consistent with current understanding of early Earth. Effects of elemental composition, pH, inclusion of catalytic montmorillonite clay, doping of chimneys with small organic compounds, and in situ ribonucleotide activation on RNA polymerization were investigated. These experiments, under certain conditions, showed successful dimerization by using unmodified ribonucleotides, with the generation of RNA oligomers up to 4 units in length when imidazole-activated ribonucleotides were used instead. Elemental analysis of the chimney precipitates and the reaction solutions showed that most of the metal cations that were determined were preferentially partitioned into the chimneys.
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Affiliation(s)
- Bradley T Burcar
- 1 New York Center for Astrobiology, Rensselaer Polytechnic Institute , Troy, New York
- 2 Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute , Troy, New York
| | - Laura M Barge
- 3 NASA Jet Propulsion Laboratory, California Institute of Technology , Pasadena, California
- 4 NASA Astrobiology Institute , Icy Worlds
| | - Dustin Trail
- 1 New York Center for Astrobiology, Rensselaer Polytechnic Institute , Troy, New York
- 5 Department of Earth and Environmental Sciences, Rensselaer Polytechnic Institute School of Science , Troy, New York
| | - E Bruce Watson
- 1 New York Center for Astrobiology, Rensselaer Polytechnic Institute , Troy, New York
- 5 Department of Earth and Environmental Sciences, Rensselaer Polytechnic Institute School of Science , Troy, New York
| | - Michael J Russell
- 3 NASA Jet Propulsion Laboratory, California Institute of Technology , Pasadena, California
- 4 NASA Astrobiology Institute , Icy Worlds
| | - Linda B McGown
- 1 New York Center for Astrobiology, Rensselaer Polytechnic Institute , Troy, New York
- 2 Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute , Troy, New York
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Burcar BT, Jawed M, Shah H, McGown LB. In situ imidazole activation of ribonucleotides for abiotic RNA oligomerization reactions. ORIGINS LIFE EVOL B 2015; 45:31-40. [PMID: 25716919 DOI: 10.1007/s11084-015-9412-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 11/13/2014] [Indexed: 11/28/2022]
Abstract
The hypothesis that RNA played a significant role in the origin of life requires effective and efficient abiotic pathways to produce RNA oligomers. The most successful abiotic oligomerization reactions to date have utilized high-energy, modified, or pre-activated ribonucleotides to generate strands of RNA up to 50-mers in length. In spite of their success, these modifications and pre-activation reactions significantly alter the ribonucleotides in ways that are highly unlikely to have occurred on a prebiotic Earth. This research seeks to address this problem by exploring an aqueous based method for activating the canonical ribonucleotides in situ using 1-Ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC) and imidazole. The reactions were run with and without a montmorillonite clay catalyst and compared to reactions that used ribonucleotides that were pre-activated with imidazole. The effects of pH and ribonucleotide concentration were also investigated. The results demonstrate the ability of in situ activation of ribonucleotides to generate linear RNA oligomers in solution, providing an alternative route to produce RNA for use in prebiotic Earth scenarios.
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Affiliation(s)
- Bradley T Burcar
- New York Center for Astrobiology and the Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, 110 8th Street Troy, New York, 12180, USA
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Feuillie C, Sverjensky DA, Hazen RM. Attachment of ribonucleotides on α-alumina as a function of pH, ionic strength, and surface loading. Langmuir 2014; 31:240-248. [PMID: 25469864 DOI: 10.1021/la504034k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The interactions between nucleic acids and mineral surfaces have been the focus of many studies in environmental sciences, in biomedicine, as well as in origin of life studies for the prebiotic formation of biopolymers. However, few studies have focused on a wide range of environmental conditions and the likely modes of attachment. Here we investigated the adsorption of ribonucleotides onto α-alumina surfaces over a wide range of pH, ionic strength, and ligand-to-solid ratio, by both an experimental and a theoretical approach. The adsorption of ribonucleotides is strongly affected by pH, with a maximum adsorption at pH values around 5. Alumina adsorbs high amounts of nucleotides >2 μmol/m(2). We used the extended triple-layer model (ETLM) to predict the speciation of the surface complexes formed as well as the stoichiometry and equilibrium constants. We propose the formation of two surface species: a monodentate inner-sphere complex, dominant at pH <7, and a bidentate outer-sphere complex, dominant at higher pH. Both complexes would involve interactions between the negatively charged phosphate group and the positively charged surface of alumina. Our results provide a better understanding of how nucleic acids attach to mineral surfaces under varying environmental conditions. Moreover, the predicted configuration of nucleotide surface species, bound via the phosphate group, could have implications for the abiotic formation of nucleic acids in the context of the origin of life.
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Affiliation(s)
- Cécile Feuillie
- Geophysical Laboratory, Carnegie Institution of Washington , 5251 Broad Branch Road North West, Washington, DC 20015, United States
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31
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Chiu HC, Koh KD, Evich M, Lesiak AL, Germann MW, Bongiorno A, Riedo E, Storici F. RNA intrusions change DNA elastic properties and structure. Nanoscale 2014; 6:10009-17. [PMID: 24992674 DOI: 10.1039/c4nr01794c] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The units of RNA, termed ribonucleoside monophosphates (rNMPs), have been recently found as the most abundant defects present in DNA. Despite the relevance, it is largely unknown if and how rNMPs embedded in DNA can change the DNA structure and mechanical properties. Here, we report that rNMPs incorporated in DNA can change the elastic properties of DNA. Atomic force microscopy (AFM)-based single molecule elasticity measurements show that rNMP intrusions in short DNA duplexes can decrease--by 32%--or slightly increase the stretch modulus of DNA molecules for two sequences reported in this study. Molecular dynamics simulations and nuclear magnetic resonance spectroscopy identify a series of significant local structural alterations of DNA containing embedded rNMPs, especially at the rNMPs and nucleotide 3' to the rNMP sites. The demonstrated ability of rNMPs to locally alter DNA mechanical properties and structure may help in understanding how such intrusions impact DNA biological functions and find applications in structural DNA and RNA nanotechnology.
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Affiliation(s)
- Hsiang-Chih Chiu
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.
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Abstract
SAICAR-mediated PKM2 protein kinase activity is necessary for EGF-induced cancer cell proliferation.
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33
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Abstract
In this issue of Molecular Cell, Keller et al. (2014) found that binding of the metabolite SAICAR to PKM2 induces the protein kinase activity of an enzyme normally designed to terminate the glycolytic pathway.
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Affiliation(s)
- Steven L McKnight
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9152, USA.
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Keller KE, Doctor ZM, Dwyer ZW, Lee YS. SAICAR induces protein kinase activity of PKM2 that is necessary for sustained proliferative signaling of cancer cells. Mol Cell 2014; 53:700-9. [PMID: 24606918 PMCID: PMC4000728 DOI: 10.1016/j.molcel.2014.02.015] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 12/24/2013] [Accepted: 01/28/2014] [Indexed: 10/25/2022]
Abstract
Abnormal metabolism and sustained proliferation are hallmarks of cancer. Pyruvate kinase M2 (PKM2) is a metabolic enzyme that plays important roles in both processes. Recently, PKM2 was shown to have protein kinase activity phosphorylating histone H3 and promoting cancer cell proliferation. However, the mechanism and extent of this protein kinase in cancer cells remain unclear. Here, we report that binding of succinyl-5-aminoimidazole-4-carboxamide-1-ribose-5'-phosphate (SAICAR), a metabolite abundant in proliferating cells, induces PKM2's protein kinase activity in vitro and in cells. Protein microarray experiments revealed that more than 100 human proteins, mostly protein kinases, are phosphorylated by PKM2-SAICAR. In particular, PKM2-SAICAR phosphorylates and activates Erk1/2, which in turn sensitizes PKM2 for SAICAR binding through phosphorylation. Additionally, PKM2-SAICAR was necessary to induce sustained Erk1/2 activation and mitogen-induced cell proliferation. Thus, the ligand-induced protein kinase activity from PKM2 is a mechanism that directly couples cell proliferation with intracellular metabolic status.
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Affiliation(s)
- Kirstie E Keller
- Department of Biology, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Zainab M Doctor
- Department of Biology, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Zachary W Dwyer
- Department of Biology, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Young-Sam Lee
- Department of Biology, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA.
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Novopashina DS, Siniakov AN, Riabinin VA, Perrouault L, Giovannangeli C, Venyaminova AG, Butorin AS. [Oligo(2'-O-Methylribonucleotides) and their derivatives: IV. Conjugates of oligo(2'-O-methylribonucleotides) with minor groove binders and intercalators: synthesis, properties and application]. Bioorg Khim 2013; 39:159-74. [PMID: 23964516 DOI: 10.1134/s1068162013010081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Conjugates of pyrimidine triplex forming 3'-protected oligo(2'-O-methylribonucleotides) with minor groove binders (MGB) and triplex specific intercalator benzoindoloquinoline (BIQ) at 5'-terminus were synthesized. The conjugates formed stable complexes with target dsDNA by simultaneous binding both in its minor and major grooves and BIQ intercalation. The dissociation constants and thermal stability of the conjugate complexes with model dsDNA corresponding to polypurine tract (PPT) of genes nef and pol from HIV proviral genome were determined. Conjugation of oligo(2'-O-methylribonucleotides) with MGB and intercalator increased the stability of the triple complexes with dsDNA at pH 7.2 and 37 degrees C. Intercalator introduction accelerates the process of complex formation. Dose-dependent arrest of the in vitro transcription was demonstrated when a 780 b.p. DNA fragment containing the polypurine tract was transcribed under the control of T7 promoter in the presence of different concentrations of conjugates of oligo(2'-O-methylribonucleotides) containing MGB and BIQ intercalator.
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36
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Makarchikov AF. [Purification and properties of a catalytically active fragment of soluble nucleoside triphosphatase from bovine kidney]. Ukr Biokhim Zh (1999) 2013; 85:31-7. [PMID: 23937046 DOI: 10.15407/ubj85.03.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
A catalytic fragment of soluble NTPase has been isolated from bovine kidneys.The 236-fold purification was carried out to obtain the preparation with a specific activity of 37.7 U/mg of protein. The purification scheme included the enzyme extraction followed by four column chromatography steps. The catalytic fragment was activated with divalent metal ions, had a pH optimum of 7.0, and possessed specificity for ITP, GTP, UTP and XTP. The apparent K(m) for Mg-ITP, Mg-GTP and Mg-UTP complexes were calculated from Hanes plots to be 1.70 mM, 0.93 mM and 0.48 mM, respectively. As estimated by gel filtration and SDS-PAAGE, the catalytic fragment has Mw 54.7 kDa being composed of two identical polypeptide chains. Our results suppose soluble NTPase from bovine kidney to consist of regulatory and catalytic structural units.
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37
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Agudelo D, Bourassa P, Beauregard M, Bérubé G, Tajmir-Riahi HA. tRNA binding to antitumor drug doxorubicin and its analogue. PLoS One 2013; 8:e69248. [PMID: 23922696 PMCID: PMC3726733 DOI: 10.1371/journal.pone.0069248] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 06/06/2013] [Indexed: 12/16/2022] Open
Abstract
The binding sites of antitumor drug doxorubicin (DOX) and its analogue N-(trifluoroacetyl) doxorubicin (FDOX) with tRNA were located, using FTIR, CD, fluorescence spectroscopic methods and molecular modeling. Different binding sites are involved in drug-tRNA adducts with DOX located in the vicinity of A-29, A-31, A-38, C-25, C-27, C-28, G-30 and U-41, while FDOX bindings involved A-23, A-44, C-25, C-27, G-24, G-42, G-53, G-45 and U-41 with similar free binding energy (-4.44 for DOX and -4.41 kcal/mol for FDOX adducts). Spectroscopic results showed that both hydrophilic and hydrophobic contacts are involved in drug-tRNA complexation and FDOX forms more stable complexes than DOX with K DOX-tRNA=4.7 (± 0.5)× 10(4) M(-1) and K FDOX-tRNA=6.3 (± 0.7)× 10(4) M(-1). The number of drug molecules bound per tRNA (n) was 0.6 for DOX and 0.4 for FDOX. No major alterations of tRNA structure were observed and tRNA remained in A-family conformation, while biopolymer aggregation and particle formation occurred at high drug concentrations.
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Affiliation(s)
- Daniel Agudelo
- Department of Chemistry and Physics, University of Québec at Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Philippe Bourassa
- Department of Chemistry and Physics, University of Québec at Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Marc Beauregard
- Department of Chemistry and Physics, University of Québec at Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Gervais Bérubé
- Department of Chemistry and Physics, University of Québec at Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Heidar-Ali Tajmir-Riahi
- Department of Chemistry and Physics, University of Québec at Trois-Rivières, Trois-Rivières, Québec, Canada
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Ritson DJ, Sutherland JD. Synthesis of aldehydic ribonucleotide and amino acid precursors by photoredox chemistry. Angew Chem Int Ed Engl 2013; 52:5845-7. [PMID: 23610046 PMCID: PMC4269183 DOI: 10.1002/anie.201300321] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Revised: 03/23/2013] [Indexed: 11/21/2022]
Affiliation(s)
- Dougal J Ritson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
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Van Laer K, Dziewulska AM, Fislage M, Wahni K, Hbeddou A, Collet JF, Versées W, Mateos LM, Tamu Dufe V, Messens J. NrdH-redoxin of Mycobacterium tuberculosis and Corynebacterium glutamicum dimerizes at high protein concentration and exclusively receives electrons from thioredoxin reductase. J Biol Chem 2013; 288:7942-7955. [PMID: 23362277 PMCID: PMC3597831 DOI: 10.1074/jbc.m112.392688] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2012] [Revised: 01/22/2013] [Indexed: 11/06/2022] Open
Abstract
NrdH-redoxins are small reductases with a high amino acid sequence similarity with glutaredoxins and mycoredoxins but with a thioredoxin-like activity. They function as the electron donor for class Ib ribonucleotide reductases, which convert ribonucleotides into deoxyribonucleotides. We solved the x-ray structure of oxidized NrdH-redoxin from Corynebacterium glutamicum (Cg) at 1.5 Å resolution. Based on this monomeric structure, we built a homology model of NrdH-redoxin from Mycobacterium tuberculosis (Mt). Both NrdH-redoxins have a typical thioredoxin fold with the active site CXXC motif located at the N terminus of the first α-helix. With size exclusion chromatography and small angle x-ray scattering, we show that Mt_NrdH-redoxin is a monomer in solution that has the tendency to form a non-swapped dimer at high protein concentration. Further, Cg_NrdH-redoxin and Mt_NrdH-redoxin catalytically reduce a disulfide with a specificity constant 1.9 × 10(6) and 5.6 × 10(6) M(-1) min(-1), respectively. They use a thiol-disulfide exchange mechanism with an N-terminal cysteine pKa lower than 6.5 for nucleophilic attack, whereas the pKa of the C-terminal cysteine is ~10. They exclusively receive electrons from thioredoxin reductase (TrxR) and not from mycothiol, the low molecular weight thiol of actinomycetes. This specificity is shown in the structural model of the complex between NrdH-redoxin and TrxR, where the two surface-exposed phenylalanines of TrxR perfectly fit into the conserved hydrophobic pocket of the NrdH-redoxin. Moreover, nrdh gene deletion and disruption experiments seem to indicate that NrdH-redoxin is essential in C. glutamicum.
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Affiliation(s)
- Koen Van Laer
- Department of Structural Biology, Vlaams Instituut voor Biotechnologie, 1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium; Brussels Center for Redox Biology, 1050 Brussels, Belgium
| | - Aleksandra M Dziewulska
- Department of Structural Biology, Vlaams Instituut voor Biotechnologie, 1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium; Brussels Center for Redox Biology, 1050 Brussels, Belgium
| | - Marcus Fislage
- Department of Structural Biology, Vlaams Instituut voor Biotechnologie, 1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Khadija Wahni
- Department of Structural Biology, Vlaams Instituut voor Biotechnologie, 1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium; Brussels Center for Redox Biology, 1050 Brussels, Belgium
| | - Abderahim Hbeddou
- Department of Structural Biology, Vlaams Instituut voor Biotechnologie, 1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium; Brussels Center for Redox Biology, 1050 Brussels, Belgium
| | - Jean-Francois Collet
- Brussels Center for Redox Biology, 1050 Brussels, Belgium; de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium; Welbio, 1200 Brussels, Belgium
| | - Wim Versées
- Department of Structural Biology, Vlaams Instituut voor Biotechnologie, 1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Luis M Mateos
- Department of Molecular Biology, Area of Microbiology, University of León, 24071 León, Spain
| | - Veronica Tamu Dufe
- Department of Structural Biology, Vlaams Instituut voor Biotechnologie, 1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium; Brussels Center for Redox Biology, 1050 Brussels, Belgium; Welbio, 1200 Brussels, Belgium
| | - Joris Messens
- Department of Structural Biology, Vlaams Instituut voor Biotechnologie, 1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium; Brussels Center for Redox Biology, 1050 Brussels, Belgium.
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40
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Kumar A, Kamaluddin. Possible role of metal(II) octacyanomolybdate(IV) in chemical evolution: interaction with ribose nucleotides. ORIGINS LIFE EVOL B 2013; 43:1-17. [PMID: 23254853 DOI: 10.1007/s11084-012-9319-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Accepted: 11/03/2012] [Indexed: 10/27/2022]
Abstract
We have proposed that double metal cyanide compounds (DMCs) might have played vital roles as catalysts in chemical evolution and the origin of life. We have synthesized a series of metal octacyanomolybdates (MOCMos) and studied their interactions with ribose nucleotides. MOCMos have been shown to be effective adsorbents for 5'-ribonucleotides. The maximum adsorption level was found to be about 50 % at neutral pH under the conditions studied. The zinc(II) octacyanomolybdate(IV) showed larger adsorption compared to other MOCMos. The surface area seems to important parameter for the adsorption of nucleotides. The adsorption followed a Langmuir adsorption isotherms with an overall adsorption trends of the order of 5'-GMP > 5'-AMP > 5'-CMP > 5'-UMP. Purine nucleotides were adsorbed more strongly than pyrimidine nucleotides on all MOCMos possibly because of the additional binding afforded by the imidazole ring in purines. Infrared spectral studies of adsorption adducts indicate that adsorption takes place through interaction between adsorbate molecules and outer divalent ions of MOCMos.
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Affiliation(s)
- Anand Kumar
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee, 247 667, U.K
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41
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Abstract
Oligoribonucleotides are potentially capable of Darwinian evolution - they may replicate and can express an independent chemical phenotype, as embodied in modern enzymatic cofactors. Using quantitative chemical kinetics on a sporadically fed ribonucleotide pool, unreliable supplies of unstable activated ribonucleotides A and B at low concentrations recurrently yield a replicating AB polymer with a potential chemical phenotype. Self-complementary replication in the pool occurs during a minority (here ≈ 35 %) of synthetic episodes that exploit coincidental overlaps between 4, 5 or 6 spikes of arbitrarily arriving substrates. Such uniquely productive synthetic episodes, in which near-ideal reaction sequences recur at random, account for most AB oligonucleotide synthesis, and therefore underlie the emergence of net replication under realistic primordial conditions. Because overlapping substrate spikes are unexpectedly frequent, and in addition, complex spike sequences appear disproportionately, a sporadically fed pool can host unexpectedly complex syntheses. Thus, primordial substrate fluctuations are not necessarily a barrier to Darwinism, but instead can facilitate early evolution.
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Affiliation(s)
- Michael Yarus
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309-0347, USA.
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42
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Abstract
Selenium derivatization of RNA is an important strategy for crystal structure determination and functional studies of noncoding RNAs and protein-RNA interactions. We describe here the synthesis of nucleoside 5'-(α-P-seleno)-triphosphate analogs (Se-NTPs) and their use in vitro transcription and purification of Se-derivatized RNA samples (phosphoroselenoate RNA, PSe-RNA).
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Affiliation(s)
- Lina Lin
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
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43
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Abstract
A testable, explicit origin for Darwinian behavior, feasible on a chaotic early Earth, would aid origins discussion. Here I show that a pool receiving unreliable supplies of unstable ribonucleotide precursors can recurrently fill this role. By using numerical integration, the differential equations governing a sporadically fed pool are solved, yielding quantitative constraints for the proliferation of molecules that also have a chemical phenotype. For example, templated triphosphate nucleotide joining is >10(4) too slow, suggesting that a group more reactive than pyrophosphate activated primordial nucleotides. However, measured literature rates are sufficient if the Initial Darwinian Ancestor (IDA) resembles a 5'-5' cofactor-like dinucleotide RNA, synthesized via activation with a phosphorimidazolide-like group. A sporadically fed pool offers unforeseen advantages; for example, the pool hosts a novel replicator which is predominantly unpaired, even though it replicates. Such free template is optimized for effective selection during its replication. Pool nucleotides are also subject to a broadly based selection that impels the population toward replication, effective selection, and Darwinian behavior. Such a primordial pool may have left detectable modern traces. A sporadically fed ribonucleotide pool also fits a recognizable early Earth environment, has recognizable modern descendants, and suits the early shape of the phylogenetic tree of Earthly life. Finally, analysis points to particular data now needed to refine the hypothesis. Accordingly, a kinetically explicit chemical hypothesis for a terran IDA can be justified, and informative experiments seem readily accessible.
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Affiliation(s)
- Michael Yarus
- Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado 80309-0347, USA.
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44
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Wang W, Wu EY, Hellinga HW, Beese LS. Structural factors that determine selectivity of a high fidelity DNA polymerase for deoxy-, dideoxy-, and ribonucleotides. J Biol Chem 2012; 287:28215-26. [PMID: 22648417 PMCID: PMC3436578 DOI: 10.1074/jbc.m112.366609] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Revised: 05/15/2012] [Indexed: 12/20/2022] Open
Abstract
In addition to discriminating against base pair mismatches, DNA polymerases exhibit a high degree of selectivity for deoxyribonucleotides over ribo- or dideoxynucleotides. It has been proposed that a single active site residue (steric gate) blocks productive binding of nucleotides containing 2'-hydroxyls. Although this steric gate plays a role in sugar moiety discrimination, its interactions do not account fully for the observed behavior of mutants. Here we present 10 high resolution crystal structures and enzyme kinetic analyses of Bacillus DNA polymerase I large fragment variants complexed with deoxy-, ribo-, and dideoxynucleotides and a DNA substrate. Taken together, these data present a more nuanced and general mechanism for nucleotide discrimination in which ensembles of intermediate conformations in the active site trap non-cognate substrates. It is known that the active site O-helix transitions from an open state in the absence of nucleotide substrates to a ternary complex closed state in which the reactive groups are aligned for catalysis. Substrate misalignment in the closed state plays a fundamental part in preventing non-cognate nucleotide misincorpation. The structures presented here show that additional O-helix conformations intermediate between the open and closed state extremes create an ensemble of binding sites that trap and misalign non-cognate nucleotides. Water-mediated interactions, absent in the fully closed state, play an important role in formation of these binding sites and can be remodeled to accommodate different non-cognate substrates. This mechanism may extend also to base pair discrimination.
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Affiliation(s)
- Weina Wang
- From the Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710
| | - Eugene Y. Wu
- From the Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710
| | - Homme W. Hellinga
- From the Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710
| | - Lorena S. Beese
- From the Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710
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45
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Palte MJ, Davis AKF, McGrath NA, Spiegel CA, Raines RT. Ribonucleoside 3'-phosphates as pro-moieties for an orally administered drug. ChemMedChem 2012; 7:1361-4. [PMID: 22807330 PMCID: PMC3516917 DOI: 10.1002/cmdc.201200243] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Revised: 06/19/2012] [Indexed: 01/14/2023]
Affiliation(s)
- Michael J Palte
- Medical Scientist Training Program and Molecular & Cellular Pharmacology Graduate Training Program, University of Wisconsin-Madison, 750 Highland Avenue, Madison, WI 53705, USA
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46
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Van Slyke GA, Ciota AT, Willsey GG, Jaeger J, Shi PY, Kramer LD. Point mutations in the West Nile virus (Flaviviridae; Flavivirus) RNA-dependent RNA polymerase alter viral fitness in a host-dependent manner in vitro and in vivo. Virology 2012; 427:18-24. [PMID: 22365326 PMCID: PMC3299857 DOI: 10.1016/j.virol.2012.01.036] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Revised: 01/14/2012] [Accepted: 01/28/2012] [Indexed: 12/18/2022]
Abstract
The West Nile virus (WNV) genome contains a single RNA-dependent RNA polymerase (RdRp) gene, which is responsible for replication of the viral genome and, as such, is an important target for antiviral therapy. Viral RdRps are known to lack proofreading capabilities and as a result viruses such as WNV exist as a mixture of viral genotypes within an infection, enabling the virus to readily emerge and adapt to new host environments. To test the consequences of subtle structural alterations remote from the RdRp active-site, the following single point mutations were engineered in the WNV NS5 RdRp coding region: T363N, A365N, and T537I; these mutations were selected in an effort to stabilize the secondary structural elements near the rNTP binding pocket of the RdRp. Mutant viruses were tested in vitro on Vero, C6/36, Culex tarsalis and DF-1 cell types and in vivo in one day old chickens and Culex pipiens mosquitoes. Plaque morphology was affected by each mutation and growth and RNA replication kinetics were altered as well. Our results demonstrate that subtle alteration of the RdRp protein away from the active site can have a significant overall biological effect on WNV fitness, and that this effect can be host-dependent.
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Affiliation(s)
- Greta A. Van Slyke
- The Arbovirus Laboratories, Wadsworth Center, New York State Dept. of Health, NY 12159
| | - Alexander T. Ciota
- The Arbovirus Laboratories, Wadsworth Center, New York State Dept. of Health, NY 12159
| | - Graham G. Willsey
- The Arbovirus Laboratories, Wadsworth Center, New York State Dept. of Health, NY 12159
| | - Joachim Jaeger
- School of Public Health, State University of New York, NY 12205
- The Center for Medical Sciences, Wadsworth Center, New York State Dept. of Health, NY 12208
| | - Pei-Yong Shi
- Novartis Institute for Tropical Disease Pte Ltd., Singapore 138670
| | - Laura D. Kramer
- The Arbovirus Laboratories, Wadsworth Center, New York State Dept. of Health, NY 12159
- School of Public Health, State University of New York, NY 12205
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47
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Aralov AV, Klykov VN, Chakhmakhcheva OG, Efimov VA. [Monomers containing 2'-o-alkoxymethyl groups as synthons for the synthesis of oligoribonucleotides by the phosphotriester method]. Bioorg Khim 2012; 37:654-61. [PMID: 22332361 DOI: 10.1134/s1068162011050025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A general scheme for the synthesis of ribonucleotide monomers containing alkoxymethyl group in 2'-O-position for the solid-phase phosphotriester oligonucleotide synthesis using O-nucleophilic intramolecular catalysis has been developed. In particular, the monomers containing 2'-O-modifying 2-azidoethoxymethyl, propargyloxymethyl, or 3,4-cyclocarbonatebutoxymethyl groups has been prepared.
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48
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Morohashi N, Kimoto M, Sato A, Kawai R, Hirao I. Site-specific incorporation of functional components into RNA by an unnatural base pair transcription system. Molecules 2012; 17:2855-76. [PMID: 22399139 PMCID: PMC6268917 DOI: 10.3390/molecules17032855] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 02/22/2012] [Accepted: 02/24/2012] [Indexed: 01/08/2023] Open
Abstract
Toward the expansion of the genetic alphabet, an unnatural base pair between 7-(2-thienyl)imidazo[4,5-b]pyridine (Ds) and pyrrole-2-carbaldehyde (Pa) functions as a third base pair in replication and transcription, and provides a useful tool for the site-specific, enzymatic incorporation of functional components into nucleic acids. We have synthesized several modified-Pa substrates, such as alkylamino-, biotin-, TAMRA-, FAM-, and digoxigenin-linked PaTPs, and examined their transcription by T7 RNA polymerase using Ds-containing DNA templates with various sequences. The Pa substrates modified with relatively small functional groups, such as alkylamino and biotin, were efficiently incorporated into RNA transcripts at the internal positions, except for those less than 10 bases from the 3′-terminus. We found that the efficient incorporation into a position close to the 3′-terminus of a transcript depended on the natural base contexts neighboring the unnatural base, and that pyrimidine-Ds-pyrimidine sequences in templates were generally favorable, relative to purine-Ds-purine sequences. The unnatural base pair transcription system provides a method for the site-specific functionalization of large RNA molecules.
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Affiliation(s)
- Nobuyuki Morohashi
- TagCyx Biotechnologies, 1-6-126 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; E-Mails: (N.M.); (M.K.); (R.K.)
| | - Michiko Kimoto
- TagCyx Biotechnologies, 1-6-126 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; E-Mails: (N.M.); (M.K.); (R.K.)
- RIKEN Systems and Structural Biology Center (SSBC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; E-Mail:
| | - Akira Sato
- RIKEN Systems and Structural Biology Center (SSBC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; E-Mail:
| | - Rie Kawai
- TagCyx Biotechnologies, 1-6-126 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; E-Mails: (N.M.); (M.K.); (R.K.)
- RIKEN Systems and Structural Biology Center (SSBC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; E-Mail:
| | - Ichiro Hirao
- TagCyx Biotechnologies, 1-6-126 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; E-Mails: (N.M.); (M.K.); (R.K.)
- RIKEN Systems and Structural Biology Center (SSBC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; E-Mail:
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +81-45-503-9644; Fax: +81-45-503-9645
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49
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Abstract
Template-directed polymerization of chemically activated ribonucleotide monomers, such as nucleotide 5'-phosphorimidazolides, has been studied as a model for nonenzymatic RNA replication during the origin of life. Kinetic studies of the polymerization of various nucleotide monomers on oligonucleotide templates have suggested that the A-form (C3'-endo sugar pucker) conformation is optimal for both monomers and templates for efficient copying. However, RNA monomers are predominantly in the C2'-endo conformation when free in solution, except for cytidine, which is approximately equally distributed between the C2'-endo and C3'-endo conformations. We hypothesized that ribonucleotides undergo a switch in sugar pucker upon binding to an A-type template and that this conformational switch allows or enhances subsequent polymerization. We used transferred nuclear Overhauser effect spectroscopy (TrNOESY), which can be used for specific detection of the bound conformation of small-molecule ligands with relatively weak affinity to receptors, to study the interactions between nucleotide 5'-phosphorimidazolides and single-stranded oligonucleotide templates. We found that the sugar pucker of activated ribonucleotides switches from C2'-endo in the free state to C3'-endo upon binding to an RNA template. This switch occurs only on RNA and not on DNA templates. Furthermore, activated 2'-deoxyribonucleotides maintain a C2'-endo sugar pucker in both the free and template-bound states. Our results provide a structural explanation for the observations that activated ribonucleotides are superior to activated deoxyribonucleotides and that RNA templates are superior to DNA templates in template-directed nonenzymatic primer-extension reactions.
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Affiliation(s)
- Na Zhang
- Howard Hughes
Medical Institute and Department of Molecular
Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street,
Boston, Massachusetts 02114, United States
| | - Shenglong Zhang
- Howard Hughes
Medical Institute and 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 and Department of Molecular
Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street,
Boston, Massachusetts 02114, United States
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50
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Thakur CS, Dayie TK. Asymmetry of 13C labeled 3-pyruvate affords improved site specific labeling of RNA for NMR spectroscopy. J Biomol NMR 2012; 52:65-77. [PMID: 22089526 PMCID: PMC3266500 DOI: 10.1007/s10858-011-9582-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2011] [Accepted: 10/10/2011] [Indexed: 05/07/2023]
Abstract
Selective isotopic labeling provides an unparalleled window within which to study the structure and dynamics of RNAs by high resolution NMR spectroscopy. Unlike commonly used carbon sources, the asymmetry of (13)C-labeled pyruvate provides selective labeling in both the ribose and base moieties of nucleotides using Escherichia coli variants, that until now were not feasible. Here we show that an E. coli mutant strain that lacks succinate and malate dehydrogenases (DL323) and grown on [3-(13)C]-pyruvate affords ribonucleotides with site specific labeling at C5' (~95%) and C1' (~42%) and minimal enrichment elsewhere in the ribose ring. Enrichment is also achieved at purine C2 and C8 (~95%) and pyrimidine C5 (~100%) positions with minimal labeling at pyrimidine C6 and purine C5 positions. These labeling patterns contrast with those obtained with DL323 E. coli grown on [1, 3-(13)C]-glycerol for which the ribose ring is labeled in all but the C4' carbon position, leading to multiplet splitting of the C1', C2' and C3' carbon atoms. The usefulness of these labeling patterns is demonstrated with a 27-nt RNA fragment derived from the 30S ribosomal subunit. Removal of the strong magnetic coupling within the ribose and base leads to increased sensitivity, substantial simplification of NMR spectra, and more precise and accurate dynamic parameters derived from NMR relaxation measurements. Thus these new labels offer valuable probes for characterizing the structure and dynamics of RNA that were previously limited by the constraint of uniformly labeled nucleotides.
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Affiliation(s)
- Chandar S. Thakur
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, 1115 Biomolecular Sciences Bldg (#296), College Park, MD 20742-3360 USA
| | - T. Kwaku Dayie
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, 1115 Biomolecular Sciences Bldg (#296), College Park, MD 20742-3360 USA
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