1
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Cohen ZR, Ding D, Zhou L, DasGupta S, Haas S, Sinclair KP, Todd ZR, Black RA, Szostak JW, Catling DC. Natural soda lakes provide compatible conditions for RNA and membrane function that could have enabled the origin of life. PNAS NEXUS 2024; 3:pgae084. [PMID: 38505692 PMCID: PMC10949909 DOI: 10.1093/pnasnexus/pgae084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 01/31/2024] [Indexed: 03/21/2024]
Abstract
The origin of life likely occurred within environments that concentrated cellular precursors and enabled their co-assembly into cells. Soda lakes (those dominated by Na+ ions and carbonate species) can concentrate precursors of RNA and membranes, such as phosphate, cyanide, and fatty acids. Subsequent assembly of RNA and membranes into cells is a long-standing problem because RNA function requires divalent cations, e.g. Mg2+, but Mg2+ disrupts fatty acid membranes. The low solubility of Mg-containing carbonates limits soda lakes to moderate Mg2+ concentrations (∼1 mM), so we investigated whether both RNAs and membranes function within these lakes. We collected water from Last Chance Lake and Goodenough Lake in Canada. Because we sampled after seasonal evaporation, the lake water contained ∼1 M Na+ and ∼1 mM Mg2+ near pH 10. In the laboratory, nonenzymatic, RNA-templated polymerization of 2-aminoimidazole-activated ribonucleotides occurred at comparable rates in lake water and standard laboratory conditions (50 mM MgCl2, pH 8). Additionally, we found that a ligase ribozyme that uses oligonucleotide substrates activated with 2-aminoimidazole was active in lake water after adjusting pH from ∼10 to 9. We also observed that decanoic acid and decanol assembled into vesicles in a dilute solution that resembled lake water after seasonal rains, and that those vesicles retained encapsulated solutes despite salt-induced flocculation when the external solution was replaced with dry-season lake water. By identifying compatible conditions for nonenzymatic and ribozyme-catalyzed RNA assembly, and for encapsulation by membranes, our results suggest that soda lakes could have enabled cellular life to emerge on Earth, and perhaps elsewhere.
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Affiliation(s)
- Zachary R Cohen
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
- Astrobiology Program, University of Washington, Seattle, WA 98195, USA
| | - Dian Ding
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Lijun Zhou
- Department of Biochemistry and Biophysics and Penn Institute for RNA Innovation, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Saurja DasGupta
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Sebastian Haas
- Astrobiology Program, University of Washington, Seattle, WA 98195, USA
- Department of Earth and Space Sciences, University of Washington, Seattle, WA 98195, USA
| | - Kimberly P Sinclair
- Astrobiology Program, University of Washington, Seattle, WA 98195, USA
- Department of Earth and Space Sciences, University of Washington, Seattle, WA 98195, USA
| | - Zoe R Todd
- Astrobiology Program, University of Washington, Seattle, WA 98195, USA
- Department of Earth and Space Sciences, University of Washington, Seattle, WA 98195, USA
- Department of Chemistry and Department of Astronomy, University of Wisconsin, Madison, WI 53706, USA
| | - Roy A Black
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
- Astrobiology Program, University of Washington, Seattle, WA 98195, USA
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - David C Catling
- Astrobiology Program, University of Washington, Seattle, WA 98195, USA
- Department of Earth and Space Sciences, University of Washington, Seattle, WA 98195, USA
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2
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Tidwell ED, Kilde IR, Leskaj S, Koutmos M. Fluorescent Ligand Equilibrium Displacement: A High-Throughput Method for Identification of FMN Riboswitch-Binding Small Molecules. Int J Mol Sci 2024; 25:735. [PMID: 38255809 PMCID: PMC11154562 DOI: 10.3390/ijms25020735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/27/2023] [Accepted: 12/28/2023] [Indexed: 01/24/2024] Open
Abstract
Antibiotic resistance remains a pressing global concern, with most antibiotics targeting the bacterial ribosome or a limited range of proteins. One class of underexplored antibiotic targets is bacterial riboswitches, structured RNA elements that regulate key biosynthetic pathways by binding a specific ligand. We developed a methodology termed Fluorescent Ligand Equilibrium Displacement (FLED) to rapidly discover small molecules that bind the flavin mononucleotide (FMN) riboswitch. FLED leverages intrinsically fluorescent FMN and the quenching effect on RNA binding to create a label-free, in vitro method to identify compounds that can bind the apo population of riboswitch in a system at equilibrium. The response difference between known riboswitch ligands and controls demonstrates the robustness of the method for high-throughput screening. An existing drug discovery library that was screened using FLED resulted in a final hit rate of 0.67%. The concentration response of each hit was determined and revealed a variety of approximate effective concentration values. Our preliminary screening data support the use of FLED to identify small molecules for medicinal chemistry development as FMN riboswitch-targeted antibiotic compounds. This robust, label-free, and cell-free method offers a strong alternative to other riboswitch screening methods and can be adapted to a variety of laboratory setups.
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Affiliation(s)
| | - Ingrid R. Kilde
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Suada Leskaj
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Markos Koutmos
- Program in Biophysics, University of Michigan, Ann Arbor, MI 48109, USA;
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA;
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA;
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3
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Lee KH, Kim S, Song J, Han SR, Kim JH, Lee SW. Efficient circular RNA engineering by end-to-end self-targeting and splicing reaction using Tetrahymena group I intron ribozyme. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:587-598. [PMID: 37637208 PMCID: PMC10457212 DOI: 10.1016/j.omtn.2023.07.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 07/28/2023] [Indexed: 08/29/2023]
Abstract
Circular RNA (circRNA) has various advantages over linear mRNA that is gaining success as a new vaccine and therapeutic agent. Thus, circRNA and its engineering methods have attracted attention recently. In this study, we developed a new in vitro circRNA engineering method by end-to-end self-targeting and splicing (STS) reaction using Tetrahymena group I intron ribozyme. We found that only the P1 helix structure of the group I intron was enough to generate circRNA by STS reaction. The efficacy of circRNA generation by STS reaction was comparable to the method using a permuted intron-exon (PIE) reaction. However, an end-to-end STS reaction does not introduce any extraneous fragments, such as an intronic scar that can be generated by PIE reaction and might trigger unwanted innate immune responses in cells, into circRNA sequences. Moreover, generated circRNA was efficiently purified by ion pair-reversed phase high-pressure liquid chromatography and used for cell-based analysis. Of note, efficient protein expression and stability with least innate immune induction by the circRNA with coxsackievirus B3 IRES were observed in cells. In conclusion, our new in vitro circRNA strategy can effectively generate highly useful circRNAs in vitro as an alternative circRNA engineering method.
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Affiliation(s)
- Kyung Hyun Lee
- R&D Center, Rznomics Inc, Seongnam 13486, Republic of Korea
| | - Seongcheol Kim
- R&D Center, Rznomics Inc, Seongnam 13486, Republic of Korea
| | - Jaehwi Song
- R&D Center, Rznomics Inc, Seongnam 13486, Republic of Korea
| | - Seung Ryul Han
- R&D Center, Rznomics Inc, Seongnam 13486, Republic of Korea
| | - Ji Hyun Kim
- R&D Center, Rznomics Inc, Seongnam 13486, Republic of Korea
| | - Seong-Wook Lee
- R&D Center, Rznomics Inc, Seongnam 13486, Republic of Korea
- Department of Bioconvergence Engineering, Research Institute of Advanced Omics, Dankook University, Yongin 16890, Republic of Korea
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4
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Hsueh BY, Ferrell MJ, Sanath-Kumar R, Bedore AM, Waters CM. Replication cycle timing determines phage sensitivity to a cytidine deaminase toxin/antitoxin bacterial defense system. PLoS Pathog 2023; 19:e1011195. [PMID: 37683045 PMCID: PMC10511110 DOI: 10.1371/journal.ppat.1011195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 09/20/2023] [Accepted: 07/21/2023] [Indexed: 09/10/2023] Open
Abstract
Toxin-antitoxin (TA) systems are ubiquitous two-gene loci that bacteria use to regulate cellular processes such as phage defense. Here, we demonstrate the mechanism by which a novel type III TA system, avcID, is activated and confers resistance to phage infection. The toxin of the system (AvcD) is a deoxycytidylate deaminase that converts deoxycytidines (dC) to dexoyuridines (dU), while the RNA antitoxin (AvcI) inhibits AvcD activity. We have shown that AvcD deaminated dC nucleotides upon phage infection, but the molecular mechanism that activated AvcD was unknown. Here we show that the activation of AvcD arises from phage-induced inhibition of host transcription, leading to degradation of the labile AvcI. AvcD activation and nucleotide depletion not only decreases phage replication but also increases the formation of defective phage virions. Surprisingly, infection of phages such as T7 that are not inhibited by AvcID also lead to AvcI RNA antitoxin degradation and AvcD activation, suggesting that depletion of AvcI is not sufficient to confer protection against some phage. Rather, our results support that phage with a longer replication cycle like T5 are sensitive to AvcID-mediated protection while those with a shorter replication cycle like T7 are resistant.
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Affiliation(s)
- Brian Y Hsueh
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
| | - Micah J Ferrell
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
| | - Ram Sanath-Kumar
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
| | - Amber M Bedore
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
| | - Christopher M Waters
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
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5
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Banna HA, Das NK, Ojha M, Koirala D. Advances in chaperone-assisted RNA crystallography using synthetic antibodies. BBA ADVANCES 2023; 4:100101. [PMID: 37655005 PMCID: PMC10466895 DOI: 10.1016/j.bbadva.2023.100101] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/13/2023] [Accepted: 08/17/2023] [Indexed: 09/02/2023] Open
Abstract
RNA molecules play essential roles in many biological functions, from gene expression regulation, cellular growth, and metabolism to catalysis. They frequently fold into three-dimensional structures to perform their functions. Therefore, determining RNA structure represents a key step for understanding the structure-function relationships and developing RNA-targeted therapeutics. X-ray crystallography remains a method of choice for determining high-resolution RNA structures, but it has been challenging due to difficulties associated with RNA crystallization and phasing. Several natural and synthetic RNA binding proteins have been used to facilitate RNA crystallography. Having unique properties to help crystal packing and phasing, synthetic antibody fragments, specifically the Fabs, have emerged as promising RNA crystallization chaperones, and so far, over a dozen of RNA structures have been solved using this strategy. Nevertheless, multiple steps in this approach need to be improved, including the recombinant expression of these anti-RNA Fabs, to warrant the full potential of these synthetic Fabs as RNA crystallization chaperones. This review highlights the nuts and bolts and recent advances in the chaperone-assisted RNA crystallography approach, specifically emphasizing the Fab antibody fragments as RNA crystallization chaperones.
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Affiliation(s)
- Hasan Al Banna
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| | - Naba Krishna Das
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| | - Manju Ojha
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| | - Deepak Koirala
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250, USA
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6
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Albers S, Allen EC, Bharti N, Davyt M, Joshi D, Perez-Garcia CG, Santos L, Mukthavaram R, Delgado-Toscano MA, Molina B, Kuakini K, Alayyoubi M, Park KJJ, Acharya G, Gonzalez JA, Sagi A, Birket SE, Tearney GJ, Rowe SM, Manfredi C, Hong JS, Tachikawa K, Karmali P, Matsuda D, Sorscher EJ, Chivukula P, Ignatova Z. Engineered tRNAs suppress nonsense mutations in cells and in vivo. Nature 2023; 618:842-848. [PMID: 37258671 PMCID: PMC10284701 DOI: 10.1038/s41586-023-06133-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 04/25/2023] [Indexed: 06/02/2023]
Abstract
Nonsense mutations are the underlying cause of approximately 11% of all inherited genetic diseases1. Nonsense mutations convert a sense codon that is decoded by tRNA into a premature termination codon (PTC), resulting in an abrupt termination of translation. One strategy to suppress nonsense mutations is to use natural tRNAs with altered anticodons to base-pair to the newly emerged PTC and promote translation2-7. However, tRNA-based gene therapy has not yielded an optimal combination of clinical efficacy and safety and there is presently no treatment for individuals with nonsense mutations. Here we introduce a strategy based on altering native tRNAs into efficient suppressor tRNAs (sup-tRNAs) by individually fine-tuning their sequence to the physico-chemical properties of the amino acid that they carry. Intravenous and intratracheal lipid nanoparticle (LNP) administration of sup-tRNA in mice restored the production of functional proteins with nonsense mutations. LNP-sup-tRNA formulations caused no discernible readthrough at endogenous native stop codons, as determined by ribosome profiling. At clinically important PTCs in the cystic fibrosis transmembrane conductance regulator gene (CFTR), the sup-tRNAs re-established expression and function in cell systems and patient-derived nasal epithelia and restored airway volume homeostasis. These results provide a framework for the development of tRNA-based therapies with a high molecular safety profile and high efficacy in targeted PTC suppression.
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Affiliation(s)
- Suki Albers
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | | | - Nikhil Bharti
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Marcos Davyt
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Disha Joshi
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA
- Children's Healthcare of Atlanta, Atlanta, GA, USA
| | | | - Leonardo Santos
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | | | | | | | | | | | | | | | | | - Amit Sagi
- Arcturus Therapeutics, San Diego, CA, USA
| | - Susan E Birket
- Pulmonary, Allergy, and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Guillermo J Tearney
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard-MIT Health Sciences and Technology, MA, Cambridge, USA
| | - Steven M Rowe
- Pulmonary, Allergy, and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Candela Manfredi
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA
- Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Jeong S Hong
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA
- Children's Healthcare of Atlanta, Atlanta, GA, USA
| | | | | | | | - Eric J Sorscher
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA.
- Children's Healthcare of Atlanta, Atlanta, GA, USA.
| | | | - Zoya Ignatova
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany.
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7
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Das NK, Hollmann NM, Vogt J, Sevdalis SE, Banna HA, Ojha M, Koirala D. Crystal structure of a highly conserved enteroviral 5' cloverleaf RNA replication element. Nat Commun 2023; 14:1955. [PMID: 37029118 PMCID: PMC10082201 DOI: 10.1038/s41467-023-37658-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 03/23/2023] [Indexed: 04/09/2023] Open
Abstract
The extreme 5'-end of the enterovirus RNA genome contains a conserved cloverleaf-like domain that recruits 3CD and PCBP proteins required for initiating genome replication. Here, we report the crystal structure at 1.9 Å resolution of this domain from the CVB3 genome in complex with an antibody chaperone. The RNA folds into an antiparallel H-type four-way junction comprising four subdomains with co-axially stacked sA-sD and sB-sC helices. Long-range interactions between a conserved A40 in the sC-loop and Py-Py helix within the sD subdomain organize near-parallel orientations of the sA-sB and sC-sD helices. Our NMR studies confirm that these long-range interactions occur in solution and without the chaperone. The phylogenetic analyses indicate that our crystal structure represents a conserved architecture of enteroviral cloverleaf-like domains, including the A40 and Py-Py interactions. The protein binding studies further suggest that the H-shape architecture provides a ready-made platform to recruit 3CD and PCBP2 for viral replication.
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Affiliation(s)
- Naba K Das
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD, 21250, USA
| | - Nele M Hollmann
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD, 21250, USA
- Howard Hughes Medical Institute, University of Maryland Baltimore County, Baltimore, MD, 21250, USA
| | - Jeff Vogt
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD, 21250, USA
| | - Spiridon E Sevdalis
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Hasan A Banna
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD, 21250, USA
| | - Manju Ojha
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD, 21250, USA
| | - Deepak Koirala
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD, 21250, USA.
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8
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Hsueh BY, Sanath-Kumar R, Bedore AM, Waters CM. Time to lysis determines phage sensitivity to a cytidine deaminase toxin/antitoxin bacterial defense system. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.09.527960. [PMID: 36798279 PMCID: PMC9934689 DOI: 10.1101/2023.02.09.527960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Toxin-antitoxin (TA) systems are ubiquitous two-gene loci that bacteria use to regulate cellular processes such as phage defense. Here, we demonstrate the mechanism by which a novel type III TA system, avcID , is activated and confers resistance to phage infection. The toxin of the system (AvcD) is a deoxycytidylate deaminase that converts deoxycytidines (dC) to dexoyuridines (dU), while the RNA antitoxin (AvcI) inhibits AvcD activity. We have shown that AvcD deaminated dC nucleotides upon phage infection, but the molecular mechanism that activated AvcD was unknown. Here we show that the activation of AvcD arises from phage-induced shutoff of host transcription, leading to degradation of the labile AvcI. AvcD activation and nucleotide depletion not only decreases phage replication but also increases the formation of defective phage virions. Surprisingly, infection of phages such as T7 that are not inhibited by AvcID also lead to AvcI RNA antitoxin degradation and AvcD activation, suggesting that depletion of AvcI is not sufficient to confer protection against some phage. Rather, our results support that phage with a longer lysis time like T5 are sensitive to AvcID-mediated protection while those with a shorter lysis time like T7 are resistant. AUTHOR’S SUMMARY Numerous diverse antiphage defense systems have been discovered in the past several years, but the mechanisms of how these systems are activated upon phage infection and why these systems protect against some phage but not others are poorly understood. The AvcID toxin-antitoxin phage defense system depletes nucleotides of the dC pool inside the host upon phage infection. We show that phage inhibition of host cell transcription activates this system by depleting the AvcI inhibitory sRNA, which inhibits production of phage and leads to the formation of defective virions. Additionally, we determined that phage lysis time is a key factor that influences sensitivity to AvcID with faster replicating phage exhibiting resistance to its effects. This study has implications for understanding the factors that influence bacterial host/phage dynamics.
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Affiliation(s)
- Brian Y. Hsueh
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA, 48824
| | - Ram Sanath-Kumar
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA, 48824
| | - Amber M. Bedore
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA, 48824
| | - Christopher M. Waters
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA, 48824
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9
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Hsueh BY, Severin GB, Elg CA, Waldron EJ, Kant A, Wessel AJ, Dover JA, Rhoades CR, Ridenhour BJ, Parent KN, Neiditch MB, Ravi J, Top EM, Waters CM. Phage defence by deaminase-mediated depletion of deoxynucleotides in bacteria. Nat Microbiol 2022; 7:1210-1220. [PMID: 35817890 PMCID: PMC9830645 DOI: 10.1038/s41564-022-01162-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 05/24/2022] [Indexed: 02/03/2023]
Abstract
Vibrio cholerae biotype El Tor is perpetuating the longest cholera pandemic in recorded history. The genomic islands VSP-1 and VSP-2 distinguish El Tor from previous pandemic V. cholerae strains. Using a co-occurrence analysis of VSP genes in >200,000 bacterial genomes we built gene networks to infer biological functions encoded in these islands. This revealed that dncV, a component of the cyclic-oligonucleotide-based anti-phage signalling system (CBASS) anti-phage defence system, co-occurs with an uncharacterized gene vc0175 that we rename avcD for anti-viral cytodine deaminase. We show that AvcD is a deoxycytidylate deaminase and that its activity is post-translationally inhibited by a non-coding RNA named AvcI. AvcID and bacterial homologues protect bacterial populations against phage invasion by depleting free deoxycytidine nucleotides during infection, thereby decreasing phage replication. Homologues of avcD exist in all three domains of life, and bacterial AvcID defends against phage infection by combining traits of two eukaryotic innate viral immunity proteins, APOBEC and SAMHD1.
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Affiliation(s)
- Brian Y Hsueh
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Geoffrey B Severin
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Clinton A Elg
- Department of Biological Sciences, Institute for Interdisciplinary Data Sciences, Bioinformatics and Computational Biology Program, University of Idaho, Moscow, ID, USA
| | - Evan J Waldron
- Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, NJ, USA
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Abhiruchi Kant
- Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, NJ, USA
| | - Alex J Wessel
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - John A Dover
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Christopher R Rhoades
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Benjamin J Ridenhour
- Department of Mathematics and Statistical Sciences, University of Idaho, Moscow, ID, USA
| | - Kristin N Parent
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Matthew B Neiditch
- Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, NJ, USA
| | - Janani Ravi
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
- Department of Pathobiology and Diagnostic Investigation, Michigan State University, East Lansing, MI, USA
| | - Eva M Top
- Department of Biological Sciences, Institute for Interdisciplinary Data Sciences, Bioinformatics and Computational Biology Program, University of Idaho, Moscow, ID, USA
| | - Christopher M Waters
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA.
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10
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Miyachi R, Shimizu Y, Ichihashi N. Transfer RNA Synthesis-Coupled Translation and DNA Replication in a Reconstituted Transcription/Translation System. ACS Synth Biol 2022; 11:2791-2799. [PMID: 35848947 DOI: 10.1021/acssynbio.2c00163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Transfer RNAs (tRNAs) are key molecules involved in translation. In vitro synthesis of tRNAs and their coupled translation are important challenges in the construction of a self-regenerative molecular system. Here, we first purified EF-Tu and ribosome components in a reconstituted translation system of Escherichia coli to remove residual tRNAs. Next, we expressed 15 types of tRNAs in the repurified translation system and performed translation of the reporter luciferase gene depending on the expression. Furthermore, we demonstrated DNA replication through expression of a tRNA encoded by DNA, mimicking information processing within the cell. Our findings highlight the feasibility of an in vitro self-reproductive system, in which tRNAs can be synthesized from replicating DNA.
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Affiliation(s)
- Ryota Miyachi
- Department of Life Science, Graduate School of Arts and Science, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Yoshihiro Shimizu
- Laboratory for Cell-Free Protein Synthesis, RIKEN Center for Biosystems Dynamics Research (BDR), Suita 565-0874, Osaka, Japan
| | - Norikazu Ichihashi
- Department of Life Science, Graduate School of Arts and Science, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan.,Komaba Institute for Science, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan.,Research Center for Complex Systems Biology, Universal Biology Institute, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
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11
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Rees HC, Gogacz W, Li NS, Koirala D, Piccirilli JA. Structural Basis for Fluorescence Activation by Pepper RNA. ACS Chem Biol 2022; 17:1866-1875. [PMID: 35759696 PMCID: PMC9969808 DOI: 10.1021/acschembio.2c00290] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pepper is a fluorogenic RNA aptamer tag that binds to a variety of benzylidene-cyanophenyl (HBC) derivatives with tight affinity and activates their fluorescence. To investigate how Pepper RNA folds to create a binding site for HBC, we used antibody-assisted crystallography to determine the structures of Pepper bound to HBC530 and HBC599 to 2.3 and 2.7 Å resolutions, respectively. The structural data show that Pepper folds into an elongated structure and organizes nucleotides within an internal bulge to create the ligand binding site, assisted by an out-of-plane platform created by tertiary interactions with an adjacent bulge. As predicted from a lack of K+ dependence, Pepper does not use a G-quadruplex to form a binding pocket for HBC. Instead, Pepper uses a unique base-quadruple·base-triple stack to sandwich the ligand with a U·G wobble pair. Site-bound Mg2+ ions support ligand binding structurally and energetically. This research provides insight into the structural features that allow the Pepper aptamer to bind HBC and show how Pepper's function may expand to allow the in vivo detection of other small molecules and metals.
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Affiliation(s)
- Huw C. Rees
- Department of Chemistry, University of Chicago, Chicago, Illinois, 60637, United States
| | - Wojciech Gogacz
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, 60637, United States
| | - Nan-Sheng Li
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, 60637, United States
| | - Deepak Koirala
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, 60637, United States
| | - Joseph A. Piccirilli
- Department of Chemistry, University of Chicago, Chicago, Illinois, 60637, United States,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, 60637, United States,corresponding author
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12
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Krochmal D, Shao Y, Li NS, DasGupta S, Shelke SA, Koirala D, Piccirilli JA. Structural basis for substrate binding and catalysis by a self-alkylating ribozyme. Nat Chem Biol 2022; 18:376-384. [PMID: 35058645 DOI: 10.1038/s41589-021-00950-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 11/23/2021] [Indexed: 12/26/2022]
Abstract
Ribozymes that react with small-molecule probes have important applications in transcriptomics and chemical biology, such as RNA labeling and imaging. Understanding the structural basis for these RNA-modifying reactions will enable the development of better tools for studying RNA. Nevertheless, high-resolution structures and underlying catalytic mechanisms for members of this ribozyme class remain elusive. Here, we focus on a self-alkylating ribozyme that catalyzes nitrogen-carbon bond formation between a specific guanine and a 2,3-disubstituted epoxide substrate and report the crystal structures of a self-alkylating ribozyme, including both alkylated and apo forms, at 1.71-Å and 2.49-Å resolution, respectively. The ribozyme assumes an elongated hairpin-like architecture preorganized to accommodate the epoxide substrate in a hook-shaped conformation. Observed reactivity of substrate analogs together with an inverse, log-linear pH dependence of the reaction rate suggests a requirement for epoxide protonation, possibly assisted by the ether oxygens within the substrate.
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Affiliation(s)
- Daniel Krochmal
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Yaming Shao
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Nan-Sheng Li
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Saurja DasGupta
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Sandip A Shelke
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Deepak Koirala
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD, USA.
| | - Joseph A Piccirilli
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA.
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.
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13
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Hyun Lee K, Kimoto M, Kawai G, Okamoto I, Fin A, Hirao I. Dye‐Conjugated Spinach RNA by Genetic Alphabet Expansion. Chemistry 2022; 28:e202104396. [DOI: 10.1002/chem.202104396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Indexed: 11/09/2022]
Affiliation(s)
- Kyung Hyun Lee
- Institute of Bioengineering and Bioimaging A*STAR 31 Biopolis Way, The Nanos #07-01 Singapore 138669 Singapore
| | - Michiko Kimoto
- Institute of Bioengineering and Bioimaging A*STAR 31 Biopolis Way, The Nanos #07-01 Singapore 138669 Singapore
| | - Gota Kawai
- Chiba Institute of Technology (CIT) Tsudanuma 2-17-1 Narashino Chiba 275-0016 Japan
| | - Itaru Okamoto
- Institute of Bioengineering and Bioimaging A*STAR 31 Biopolis Way, The Nanos #07-01 Singapore 138669 Singapore
| | - Andrea Fin
- Institute of Bioengineering and Bioimaging A*STAR 31 Biopolis Way, The Nanos #07-01 Singapore 138669 Singapore
| | - Ichiro Hirao
- Institute of Bioengineering and Bioimaging A*STAR 31 Biopolis Way, The Nanos #07-01 Singapore 138669 Singapore
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14
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Narayan C, Veeramani S, Thiel WH. Optimization of RNA Aptamer SELEX Methods: Improved Aptamer Transcript 3'-End Homogeneity, PAGE Purification Yield, and Target-Bound Aptamer RNA Recovery. Nucleic Acid Ther 2022; 32:74-80. [PMID: 34757856 PMCID: PMC8817694 DOI: 10.1089/nat.2021.0060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Since its inception in the early 1990s, SELEX remains the gold standard for discovering RNA aptamers specific for proteins and small molecules. The SELEX process has undergone countless modifications and now encompasses a breadth of innovative selection schemes to pare an aptamer library toward target-specific aptamers. Common to all these RNA aptamer SELEX processes are the steps for the preparation of DNA template and in vitro transcription of aptamer RNA. These steps have remained mostly unchanged over the past three decades and would benefit from optimization. We focused on three key areas: improving the homogeneity of in vitro transcribed aptamer RNA, increasing the efficiency of in vitro transcribed aptamer RNA purification by PAGE, and improving the quality of target-bound aptamer RNA recovered during SELEX. Together, these optimizations contribute toward a more efficient SELEX process and are applicable to both protein-based and cell-based RNA aptamer selections.
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Affiliation(s)
- Chandan Narayan
- Department of Internal Medicine and University of Iowa, Iowa City, Iowa, USA
| | - Suresh Veeramani
- Department of Internal Medicine and University of Iowa, Iowa City, Iowa, USA.,Department of Holden Comprehensive Cancer Center, University of Iowa, Iowa City, Iowa, USA.,Address correspondence to: Suresh Veeramani, DVM, PhD, Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - William H. Thiel
- Department of Internal Medicine and University of Iowa, Iowa City, Iowa, USA.,Address correspondence to: William H. Thiel, PhD, Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
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15
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Abstract
In recent years, it has become clear that RNA molecules are involved in almost all vital cellular processes and pathogenesis of human disorders. The functional diversity of RNA comes from its structural richness. Although composed of only four nucleotides, RNA molecules present a plethora of secondary and tertiary structures critical for intra and intermolecular contacts with other RNAs and ligands (proteins, small metabolites, etc.). In order to fully understand RNA function it is necessary to define its spatial structure. Crystallography, nuclear magnetic resonance and cryogenic electron microscopy have demonstrated considerable success in determining the structures of biologically important RNA molecules. However, these powerful methods require large amounts of sample. Despite their limitations, chemical synthesis and in vitro transcription are usually employed to obtain milligram quantities of RNA for structural studies, delivering simple and effective methods for large-scale production of homogenous samples. The aim of this paper is to provide an overview of methods for large-scale RNA synthesis with emphasis on chemical synthesis and in vitro transcription. We also present our own results of testing the efficiency of these approaches in order to adapt the material acquisition strategy depending on the desired RNA construct.
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16
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High Affinity Binding of N2-Modified Guanine Derivatives Significantly Disrupts the Ligand Binding Pocket of the Guanine Riboswitch. Molecules 2020; 25:molecules25102295. [PMID: 32414072 PMCID: PMC7287874 DOI: 10.3390/molecules25102295] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/10/2020] [Accepted: 05/12/2020] [Indexed: 11/17/2022] Open
Abstract
Riboswitches are important model systems for the development of approaches to search for RNA-targeting therapeutics. A principal challenge in finding compounds that target riboswitches is that the effector ligand is typically almost completely encapsulated by the RNA, which severely limits the chemical space that can be explored. Efforts to find compounds that bind the guanine/adenine class of riboswitches with a high affinity have in part focused on purines modified at the C6 and C2 positions. These studies have revealed compounds that have low to sub-micromolar affinity and, in a few cases, have antimicrobial activity. To further understand how these compounds interact with the guanine riboswitch, we have performed an integrated structural and functional analysis of representative guanine derivatives with modifications at the C8, C6 and C2 positions. Our data indicate that while modifications of guanine at the C6 position are generally unfavorable, modifications at the C8 and C2 positions yield compounds that rival guanine with respect to binding affinity. Surprisingly, C2-modified guanines such as N2-acetylguanine completely disrupt a key Watson–Crick pairing interaction between the ligand and RNA. These compounds, which also modulate transcriptional termination as efficiently as guanine, open up a significant new chemical space of guanine modifications in the search for antimicrobial agents that target purine riboswitches.
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17
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Matyjasik MM, Batey RT. Structural basis for 2'-deoxyguanosine recognition by the 2'-dG-II class of riboswitches. Nucleic Acids Res 2020; 47:10931-10941. [PMID: 31598729 PMCID: PMC6847200 DOI: 10.1093/nar/gkz839] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 09/12/2019] [Accepted: 10/05/2019] [Indexed: 12/25/2022] Open
Abstract
A recent bioinformatic analysis of well-characterized classes of riboswitches uncovered subgroups unable to bind to the regulatory molecule of the parental class. Within the guanine/adenine class, seven groups of RNAs were identified that deviate from the consensus sequence at one or more of three positions directly involved purine nucleobase recognition, one of which was validated as a second class of 2'-deoxyguanosine riboswitch (called 2'-dG-II). To understand how 2'-dG-II riboswitches recognize their cognate ligand and how they differ from a previously identified class of 2'-deoxyguanosine binding riboswitches, we have solved the crystal structure of a 2'-dG-II aptamer domain bound to 2'-deoxyguanosine. This structure reveals a global architecture similar to other members of the purine riboswitch family, but contains key differences within the ligand binding core. Defining the 2'-dG-II riboswitches is a two-nucleotide insertion in the three-way junction that promotes novel base-base interactions. Unlike 2'-dG-I riboswitches, the 2'-dG-II class only requires local changes to the ligand binding pocket of the guanine/adenine class to achieve a change in ligand preference. Notably, members of the 2'-dG-II family have variable ability to discriminate between 2'-deoxyguanosine and riboguanosine, suggesting that a subset of 2'-dG-II riboswitches may bind either molecule to regulate gene expression.
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Affiliation(s)
- Michal M Matyjasik
- Department of Biochemistry, University of Colorado at Boulder, Campus Box 596, Boulder, CO 80309-0596, USA
| | - Robert T Batey
- Department of Biochemistry, University of Colorado at Boulder, Campus Box 596, Boulder, CO 80309-0596, USA
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18
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Hammerling MJ, Krüger A, Jewett MC. Strategies for in vitro engineering of the translation machinery. Nucleic Acids Res 2020; 48:1068-1083. [PMID: 31777928 PMCID: PMC7026604 DOI: 10.1093/nar/gkz1011] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 10/07/2019] [Accepted: 10/17/2019] [Indexed: 01/06/2023] Open
Abstract
Engineering the process of molecular translation, or protein biosynthesis, has emerged as a major opportunity in synthetic and chemical biology to generate novel biological insights and enable new applications (e.g. designer protein therapeutics). Here, we review methods for engineering the process of translation in vitro. We discuss the advantages and drawbacks of the two major strategies-purified and extract-based systems-and how they may be used to manipulate and study translation. Techniques to engineer each component of the translation machinery are covered in turn, including transfer RNAs, translation factors, and the ribosome. Finally, future directions and enabling technological advances for the field are discussed.
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Affiliation(s)
- Michael J Hammerling
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Antje Krüger
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
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19
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Koirala D, Lewicka A, Koldobskaya Y, Huang H, Piccirilli JA. Synthetic Antibody Binding to a Preorganized RNA Domain of Hepatitis C Virus Internal Ribosome Entry Site Inhibits Translation. ACS Chem Biol 2020; 15:205-216. [PMID: 31765566 DOI: 10.1021/acschembio.9b00785] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Structured RNA elements within the internal ribosome entry site (IRES) of hepatitis C virus (HCV) genome hijack host cell machinery for translation initiation through a cap-independent mechanism. Here, using a phage display selection, we obtained two antibody fragments (Fabs), HCV2 and HCV3, against HCV IRES that bind the RNA with dissociation constants of 32 ± 7 nM and 37 ± 8 nM respectively, specifically recognizing the so-called junction IIIabc (JIIIabc). We used these Fabs as crystallization chaperones and determined the high-resolution crystal structures of JIIIabc-HCV2 and -HCV3 complexes at 1.81 Å and 2.75 Å resolution respectively, revealing an antiparallel four-way junction with the IIIa and IIIc subdomains brought together through tertiary interactions. The RNA conformation observed in the structures supports the structural model for this region derived from cryo-EM data for the HCV IRES-40S ribosome complex, suggesting that the tertiary fold of the RNA preorganizes the domain for interactions with the 40S ribosome. Strikingly, both Fabs and the ribosomal protein eS27 not only interact with a common subset of nucleotides within the JIIIabc but also use physiochemically similar sets of protein residues to do so, suggesting that the RNA surface is well-suited for interactions with proteins, perhaps analogous to the "hot spot" concept elaborated for protein-protein interactions. Using a rabbit reticulocyte lysate-based translation assay with a bicistronic reporter construct, we further demonstrated that Fabs HCV2 and HCV3 specifically inhibit the HCV IRES-directed translation, implicating disruption of the JIIIabc-ribosome interaction as a potential therapeutic strategy against HCV.
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Affiliation(s)
- Deepak Koirala
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, United States
| | - Anna Lewicka
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, United States
| | - Yelena Koldobskaya
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, United States
| | - Hao Huang
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, United States
| | - Joseph A. Piccirilli
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, United States
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
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20
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Koirala D, Shao Y, Koldobskaya Y, Fuller JR, Watkins AM, Shelke SA, Pilipenko EV, Das R, Rice PA, Piccirilli JA. A conserved RNA structural motif for organizing topology within picornaviral internal ribosome entry sites. Nat Commun 2019; 10:3629. [PMID: 31399592 PMCID: PMC6689051 DOI: 10.1038/s41467-019-11585-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 07/09/2019] [Indexed: 12/30/2022] Open
Abstract
Picornaviral IRES elements are essential for initiating the cap-independent viral translation. However, three-dimensional structures of these elements remain elusive. Here, we report a 2.84-Å resolution crystal structure of hepatitis A virus IRES domain V (dV) in complex with a synthetic antibody fragment-a crystallization chaperone. The RNA adopts a three-way junction structure, topologically organized by an adenine-rich stem-loop motif. Despite no obvious sequence homology, the dV architecture shows a striking similarity to a circularly permuted form of encephalomyocarditis virus J-K domain, suggesting a conserved strategy for organizing the domain architecture. Recurrence of the motif led us to use homology modeling tools to compute a 3-dimensional structure of the corresponding domain of foot-and-mouth disease virus, revealing an analogous domain organizing motif. The topological conservation observed among these IRESs and other viral domains implicates a structured three-way junction as an architectural scaffold to pre-organize helical domains for recruiting the translation initiation machinery.
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Affiliation(s)
- Deepak Koirala
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Yaming Shao
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Yelena Koldobskaya
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - James R Fuller
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Andrew M Watkins
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Sandip A Shelke
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Evgeny V Pilipenko
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Rhiju Das
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Phoebe A Rice
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Joseph A Piccirilli
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA.
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA.
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21
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Molina-Sánchez MD, Toro N. DNA cleavage and reverse splicing of ribonucleoprotein particles reconstituted in vitro with linear RmInt1 RNA. RNA Biol 2019; 16:930-939. [PMID: 30943851 DOI: 10.1080/15476286.2019.1601379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
The RmInt1 group II intron is an efficient self-splicing mobile retroelement that catalyzes its own excision as lariat, linear and circular molecules. In vivo, the RmInt1 lariat and the reverse transcriptase (IEP) it encodes form a ribonucleoprotein particle (RNP) that recognizes the DNA target for site-specific full intron insertion via a two-step reverse splicing reaction. RNPs containing linear group II intron RNA are generally thought to be unable to complete the reverse splicing reaction. Here, we show that reconstituted in vitro RNPs containing linear RmInt1 ΔORF RNA can mediate the cleavage of single-stranded DNA substrates in a very precise manner with the attachment of the intron RNA to the 3´exon as the first step of a reverse splicing reaction. Notably, we also observe molecules in which the 5´exon is linked to the RmInt1 RNA, suggesting the completion of the reverse splicing reaction, albeit rather low and inefficiently. That process depends on DNA target recognition and can be successful completed by RmInt1 RNPs with linear RNA displaying 5´ modifications.
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Affiliation(s)
- María Dolores Molina-Sánchez
- a Structure, Dynamics and Function of Rhizobacterial Genomes, Grupo de Ecología Genética de la Rizosfera, Department of Soil Microbiology and Symbiotic Systems , Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas , Granada , Spain
| | - Nicolás Toro
- a Structure, Dynamics and Function of Rhizobacterial Genomes, Grupo de Ecología Genética de la Rizosfera, Department of Soil Microbiology and Symbiotic Systems , Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas , Granada , Spain
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22
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Shelke SA, Shao Y, Laski A, Koirala D, Weissman BP, Fuller JR, Tan X, Constantin TP, Waggoner AS, Bruchez MP, Armitage BA, Piccirilli JA. Structural basis for activation of fluorogenic dyes by an RNA aptamer lacking a G-quadruplex motif. Nat Commun 2018; 9:4542. [PMID: 30382099 PMCID: PMC6208384 DOI: 10.1038/s41467-018-06942-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 09/26/2018] [Indexed: 12/24/2022] Open
Abstract
The DIR2s RNA aptamer, a second-generation, in-vitro selected binder to dimethylindole red (DIR), activates the fluorescence of cyanine dyes, DIR and oxazole thiazole blue (OTB), allowing detection of two well-resolved emission colors. Using Fab BL3-6 and its cognate hairpin as a crystallization module, we solved the crystal structures of both the apo and OTB-SO3 bound forms of DIR2s at 2.0 Å and 1.8 Å resolution, respectively. DIR2s adopts a compact, tuning fork-like architecture comprised of a helix and two short stem-loops oriented in parallel to create the ligand binding site through tertiary interactions. The OTB-SO3 fluorophore binds in a planar conformation to a claw-like structure formed by a purine base-triple, which provides a stacking platform for OTB-SO3, and an unpaired nucleotide, which partially caps the binding site from the top. The absence of a G-quartet or base tetrad makes the DIR2s aptamer unique among fluorogenic RNAs with known 3D structure. The DIR2s RNA aptamer activates the fluorescence of cyanine dyes allowing detection of two well-resolved emission colors. Here authors solve the crystal structures of the apo and OTB-SO3 fluorophore-bound DIR2s and show how the fluorophore ligand is bound.
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Affiliation(s)
- Sandip A Shelke
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Yaming Shao
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Artur Laski
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Deepak Koirala
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | | | - James R Fuller
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Xiaohong Tan
- Center for Nucleic Acids Science and Technology, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.,Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Tudor P Constantin
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Alan S Waggoner
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.,Molecular Biosensor and Imaging Center, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Marcel P Bruchez
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.,Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.,Molecular Biosensor and Imaging Center, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Bruce A Armitage
- Center for Nucleic Acids Science and Technology, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.,Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Joseph A Piccirilli
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA. .,Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA.
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23
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Pechlaner M, Dominguez-Martin A, Sigel RKO. Influence of pH and Mg(ii) on the catalytic core domain 5 of a bacterial group II intron. Dalton Trans 2018; 46:3989-3995. [PMID: 28265619 DOI: 10.1039/c6dt04784j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
RNA molecules fold into complex structures that allow them to perform specific functions. To compensate the relative lack of diversity of functional groups within nucleotides, metal ions work as crucial co-factors. In addition, shifted pKas are observed in RNA, enabling acid-base reactions at ambient pH. The central catalytic domain 5 (D5) hairpin of the Azotobacter vinelandii group II intron undergoes both metal ion binding and pH dependence, presumably playing an important functional role in the ribozyme's reaction. By NMR spectroscopy we have here characterized the metal ion binding sites and affinities for the hairpin's internal G-A mismatch, bulge, and pentaloop. The influence of Mg(ii) and pH on the local conformation of the catalytically crucial region is also explored by fluorescence spectroscopy.
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Affiliation(s)
- M Pechlaner
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, Zurich, Switzerland.
| | - A Dominguez-Martin
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, Zurich, Switzerland.
| | - R K O Sigel
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, Zurich, Switzerland.
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24
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Lightfoot HL, Hagen T, Cléry A, Allain FHT, Hall J. Control of the polyamine biosynthesis pathway by G 2-quadruplexes. eLife 2018; 7:e36362. [PMID: 30063205 PMCID: PMC6067879 DOI: 10.7554/elife.36362] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 06/13/2018] [Indexed: 12/16/2022] Open
Abstract
G-quadruplexes are naturally-occurring structures found in RNAs and DNAs. Regular RNA G-quadruplexes are highly stable due to stacked planar arrangements connected by short loops. However, reports of irregular quadruplex structures are increasing and recent genome-wide studies suggest that they influence gene expression. We have investigated a grouping of G2-motifs in the UTRs of eight genes involved in polyamine biosynthesis, and concluded that several likely form novel metastable RNA G-quadruplexes. We performed a comprehensive biophysical characterization of their properties, comparing them to a reference G-quadruplex. Using cellular assays, together with polyamine-depleting and quadruplex-stabilizing ligands, we discovered how some of these motifs regulate and sense polyamine levels, creating feedback loops during polyamine biosynthesis. Using high-resolution 1H-NMR spectroscopy, we demonstrated that a long-looped quadruplex in the AZIN1 mRNA co-exists in salt-dependent equilibria with a hairpin structure. This study expands the repertoire of regulatory G-quadruplexes and demonstrates how they act in unison to control metabolite homeostasis.
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Affiliation(s)
- Helen Louise Lightfoot
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical SciencesETH ZurichZurichSwitzerland
| | - Timo Hagen
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical SciencesETH ZurichZurichSwitzerland
| | - Antoine Cléry
- Department of Biology, Institute of Molecular Biology and BiophysicsETH ZurichZurichSwitzerland
- Biomolecular NMR spectroscopy platformETH ZurichZurichSwitzerland
| | | | - Jonathan Hall
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical SciencesETH ZurichZurichSwitzerland
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25
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Koirala D, Shelke SA, Dupont M, Ruiz S, DasGupta S, Bailey LJ, Benner SA, Piccirilli JA. Affinity maturation of a portable Fab-RNA module for chaperone-assisted RNA crystallography. Nucleic Acids Res 2018; 46:2624-2635. [PMID: 29309709 PMCID: PMC5861428 DOI: 10.1093/nar/gkx1292] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 12/13/2017] [Accepted: 12/28/2017] [Indexed: 12/13/2022] Open
Abstract
Antibody fragments such as Fabs possess properties that can enhance protein and RNA crystallization and therefore can facilitate macromolecular structure determination. In particular, Fab BL3-6 binds to an AAACA RNA pentaloop closed by a GC pair with ∼100 nM affinity. The Fab and hairpin have served as a portable module for RNA crystallization. The potential for general application make it desirable to adjust the properties of this crystallization module in a manner that facilitates its use for RNA structure determination, such as ease of purification, surface entropy or binding affinity. In this work, we used both in vitro RNA selection and phage display selection to alter the epitope and paratope sides of the binding interface, respectively, for improved binding affinity. We identified a 5'-GNGACCC-3' consensus motif in the RNA and S97N mutation in complimentarity determining region L3 of the Fab that independently impart about an order of magnitude improvement in affinity, resulting from new hydrogen bonding interactions. Using a model RNA, these modifications facilitated crystallization under a wider range of conditions and improved diffraction. The improved features of the Fab-RNA module may facilitate its use as an affinity tag for RNA purification and imaging and as a chaperone for RNA crystallography.
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Affiliation(s)
- Deepak Koirala
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Sandip A Shelke
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Marcel Dupont
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Stormy Ruiz
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
| | - Saurja DasGupta
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
| | - Lucas J Bailey
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Alachua, FL 32615, USA
| | - Joseph A Piccirilli
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
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26
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DasGupta S, Suslov NB, Piccirilli JA. Structural Basis for Substrate Helix Remodeling and Cleavage Loop Activation in the Varkud Satellite Ribozyme. J Am Chem Soc 2017; 139:9591-9597. [PMID: 28625058 PMCID: PMC5929484 DOI: 10.1021/jacs.7b03655] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The Varkud satellite (VS) ribozyme catalyzes site-specific RNA cleavage and ligation reactions. Recognition of the substrate involves a kissing loop interaction between the substrate and the catalytic domain of the ribozyme, resulting in a rearrangement of the substrate helix register into a so-called "shifted" conformation that is critical for substrate binding and activation. We report a 3.3 Å crystal structure of the complete ribozyme that reveals the active, shifted conformation of the substrate, docked into the catalytic domain of the ribozyme. Comparison to previous NMR structures of isolated, inactive substrates provides a physical description of substrate remodeling, and implicates roles for tertiary interactions in catalytic activation of the cleavage loop. Similarities to the hairpin ribozyme cleavage loop activation suggest general strategies to enhance fidelity in RNA folding and ribozyme cleavage.
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Affiliation(s)
- Saurja DasGupta
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
| | - Nikolai B. Suslov
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Joseph A. Piccirilli
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
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27
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Bartova S, Alberti E, Sigel RK, Donghi D. Metal ion binding to an RNA internal loop. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2016.02.050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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28
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Bartova S, Pechlaner M, Donghi D, Sigel RKO. Studying metal ion binding properties of a three-way junction RNA by heteronuclear NMR. J Biol Inorg Chem 2016; 21:319-28. [PMID: 26880094 DOI: 10.1007/s00775-016-1341-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 01/25/2016] [Indexed: 10/22/2022]
Abstract
Self-splicing group II introns are highly structured RNA molecules, containing a characteristic secondary and catalytically active tertiary structure, which is formed only in the presence of Mg(II). Mg(II) initiates the first folding step governed by the κζ element within domain 1 (D1κζ). We recently solved the NMR structure of D1κζ derived from the mitochondrial group II intron ribozyme Sc.ai5γ and demonstrated that Mg(II) is essential for its stabilization. Here, we performed a detailed multinuclear NMR study of metal ion interactions with D1κζ, using Cd(II) and cobalt(III)hexammine to probe inner- and outer-sphere coordination of Mg(II) and thus to better characterize its binding sites. Accordingly, we mapped (1)H, (15)N, (13)C, and (31)P spectral changes upon addition of different amounts of the metal ions. Our NMR data reveal a Cd(II)-assisted macrochelate formation at the 5'-end triphosphate, a preferential Cd(II) binding to guanines in a helical context, an electrostatic interaction in the ζ tetraloop receptor and various metal ion interactions in the GAAA tetraloop and κ element. These results together with our recently published data on Mg(II) interaction provide a much better understanding of Mg(II) binding to D1κζ, and reveal how intricate and complex metal ion interactions can be.
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Affiliation(s)
- Simona Bartova
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.,Department of Analytical Chemistry, University of Chemistry and Technology Prague, Technická 5, 166 28, Prague, Czech Republic
| | - Maria Pechlaner
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.,Institute for Molecular Modeling and Simulation, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria
| | - Daniela Donghi
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
| | - Roland K O Sigel
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
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29
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Someya T, Ando A, Kimoto M, Hirao I. Site-specific labeling of RNA by combining genetic alphabet expansion transcription and copper-free click chemistry. Nucleic Acids Res 2015; 43:6665-76. [PMID: 26130718 PMCID: PMC4538826 DOI: 10.1093/nar/gkv638] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 06/10/2015] [Indexed: 12/16/2022] Open
Abstract
Site-specific labeling of long-chain RNAs with desired molecular probes is an imperative technique to facilitate studies of functional RNA molecules. By genetic alphabet expansion using an artificial third base pair, called an unnatural base pair, we present a post-transcriptional modification method for RNA transcripts containing an incorporated azide-linked unnatural base at specific positions, using a copper-free click reaction. The unnatural base pair between 7-(2-thienyl)imidazo[4,5-b]pyridine (Ds) and pyrrole-2-carbaldehyde (Pa) functions in transcription. Thus, we chemically synthesized a triphosphate substrate of 4-(4-azidopentyl)-pyrrole-2-carbaldehyde (N3-PaTP), which can be site-specifically introduced into RNA, opposite Ds in templates by T7 transcription. The N3-Pa incorporated in the transcripts was modified with dibenzocyclooctyne (DIBO) derivatives. We demonstrated the transcription of 17-, 76- and 260-mer RNA molecules and their site-specific labeling with Alexa 488, Alexa 594 and biotin. This method will be useful for preparing RNA molecules labeled with any functional groups of interest, toward in vivo experiments.
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Affiliation(s)
- Tatsuhiko Someya
- RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Ami Ando
- RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Michiko Kimoto
- RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan TagCyx Biotechnologies, 1-6-126 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan PRESTO, JST, Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Ichiro Hirao
- RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan TagCyx Biotechnologies, 1-6-126 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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30
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D'Heygère F, Schwartz A, Coste F, Castaing B, Boudvillain M. Monitoring RNA unwinding by the transcription termination factor Rho from Mycobacterium tuberculosis. Methods Mol Biol 2015; 1259:293-311. [PMID: 25579593 DOI: 10.1007/978-1-4939-2214-7_18] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Transcription termination factor Rho is a ring-shaped, homo-hexamieric RNA translocase that dissociates transcription elongation complexes and transcriptional RNA-DNA duplexes (R-loops) in bacteria. The molecular mechanisms underlying these biological functions have been essentially studied with Rho enzymes from Escherichia coli or close Gram-negative relatives. However, phylo-divergent Rho factors may have distinct properties. Here, we describe methods for the preparation and in vitro characterization (ATPase and helicase activities) of the Rho factor from Mycobacterium tuberculosis, a specimen with uncharacteristic molecular and enzymatic features. These methods set the stage for future studies aimed at better defining the diversity of enzymatic properties of Rho across the bacterial kingdom.
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Affiliation(s)
- François D'Heygère
- Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique (CNRS), Rue Charles Sadron, 45071, Orléans, cedex 2, France
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31
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Samanta A, Krause A, Jäschke A. A modified dinucleotide for site-specific RNA-labelling by transcription priming and click chemistry. Chem Commun (Camb) 2014; 50:1313-6. [PMID: 24343756 DOI: 10.1039/c3cc46132g] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An improved strategy for RNA labelling using an alkyne-carrying dinucleotide is reported. This involves near-quantitative priming by phage RNA-polymerases followed by conjugation of different labels using click chemistry. Moreover, these transcripts bear a ligation compatible 5'-end, and thus through ligation the terminal label can be transformed to an internal one.
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Affiliation(s)
- Ayan Samanta
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, Heidelberg 69120, Germany.
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32
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Huang H, Suslov NB, Li NS, Shelke SA, Evans ME, Koldobskaya Y, Rice PA, Piccirilli JA. A G-quadruplex-containing RNA activates fluorescence in a GFP-like fluorophore. Nat Chem Biol 2014; 10:686-91. [PMID: 24952597 PMCID: PMC4104137 DOI: 10.1038/nchembio.1561] [Citation(s) in RCA: 236] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 05/21/2014] [Indexed: 01/30/2023]
Abstract
Spinach is an in vitro-selected RNA aptamer that binds a GFP-like ligand and activates its green fluorescence. Spinach is thus an RNA analog of GFP and has potentially widespread applications for in vivo labeling and imaging. We used antibody-assisted crystallography to determine the structures of Spinach both with and without bound fluorophore at 2.2-Å and 2.4-Å resolution, respectively. Spinach RNA has an elongated structure containing two helical domains separated by an internal bulge that folds into a G-quadruplex motif of unusual topology. The G-quadruplex motif and adjacent nucleotides comprise a partially preformed binding site for the fluorophore. The fluorophore binds in a planar conformation and makes extensive aromatic stacking and hydrogen bond interactions with the RNA. Our findings provide a foundation for structure-based engineering of new fluorophore-binding RNA aptamers.
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Affiliation(s)
- Hao Huang
- Department of Chemistry, University of Chicago, Chicago, IL, 60637, USA
| | - Nikolai B. Suslov
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Nan-Sheng Li
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Sandip A. Shelke
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Molly E. Evans
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | | | - Phoebe A. Rice
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Joseph A. Piccirilli
- Department of Chemistry, University of Chicago, Chicago, IL, 60637, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
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33
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Solution structure and metal ion binding sites of the human CPEB3 ribozyme's P4 domain. J Biol Inorg Chem 2014; 19:903-12. [PMID: 24652468 DOI: 10.1007/s00775-014-1125-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Accepted: 03/05/2014] [Indexed: 01/18/2023]
Abstract
Three ribozymes are known to occur in humans, the CPEB3 ribozyme, the CoTC ribozyme, and the hammerhead ribozyme. Here, we present the NMR solution structure of a well-conserved motif within the CPEB3 ribozyme, the P4 domain. In addition, we discuss the binding sites and impact of Mg(2+) and [Co(NH3)6](3+), a spectroscopic probe for [Mg(H2O)6](2+), on the structure. The well-defined P4 region is a hairpin closed with a UGGU tetraloop that shows a distinct electrostatic surface potential and a characteristic, strongly curved backbone trajectory. The P4 hairpin contains two specific Mg(2+) binding sites: one outer-sphere binding site close to the proposed CPEB3 ribozyme active site with potential relevance for maintaining a compact fold of the ribozyme core, and one inner-sphere binding site, probably stabilizing the tetraloop structure. The structure of the tetraloop resembles an RNase III recognition structure, as previously described for an AGUU tetraloop. The detailed knowledge of the P4 domain and its metal ion binding preferences thus brings us closer to understanding the importance of Mg(2+) binding for the CPEB3 ribozyme's fold and function in the cell.
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34
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Advances in methods for native expression and purification of RNA for structural studies. Curr Opin Struct Biol 2014; 26:1-8. [PMID: 24607442 DOI: 10.1016/j.sbi.2014.01.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Revised: 01/22/2014] [Accepted: 01/28/2014] [Indexed: 11/23/2022]
Abstract
Many RNAs present unique challenges in obtaining material suitable for structural or biophysical characterization. These issues include synthesis of chemically and conformationally homogeneous RNAs, refolding RNA purified using denaturing preparation techniques, and avoiding chemical damage. To address these challenges, new methodologies in RNA expression and purification have been developed seeking to emulate those commonly used for proteins. In this review, recent developments in the preparation of high-quality RNA for structural biology and biophysical applications are discussed, with an emphasis on native methods.
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35
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The kinetics of ribozyme cleavage: a tool to analyze RNA folding as a function of catalysis. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2013; 1086:209-24. [PMID: 24136606 DOI: 10.1007/978-1-62703-667-2_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
As catalytically active RNAs, ribozymes can be characterized by kinetic measurements similar to classical enzyme kinetics. However, in contrast to standard protein enzymes, for which reactions can usually be started by mixing the enzyme with its substrate, ribozymes are typically self-cleaving. The reaction has to be initiated by folding the RNA into its active conformation. Thus, ribozyme kinetics are influenced by both folding and catalytic components and often enable indirect observation of RNA folding. Here, I describe how to obtain quantitative ribozyme cleavage data via denaturing polyacrylamide gel electrophoresis (PAGE) of radioactively labeled in vitro transcripts and discuss general considerations for subsequent kinetic analysis.
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36
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RNA polymerase II acts as an RNA-dependent RNA polymerase to extend and destabilize a non-coding RNA. EMBO J 2013; 32:781-90. [PMID: 23395899 DOI: 10.1038/emboj.2013.18] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Accepted: 01/03/2013] [Indexed: 11/09/2022] Open
Abstract
RNA polymerase II (Pol II) is a well-characterized DNA-dependent RNA polymerase, which has also been reported to have RNA-dependent RNA polymerase (RdRP) activity. Natural cellular RNA substrates of mammalian Pol II, however, have not been identified and the cellular function of the Pol II RdRP activity is unknown. We found that Pol II can use a non-coding RNA, B2 RNA, as both a substrate and a template for its RdRP activity. Pol II extends B2 RNA by 18 nt on its 3'-end in an internally templated reaction. The RNA product resulting from extension of B2 RNA by the Pol II RdRP can be removed from Pol II by a factor present in nuclear extracts. Treatment of cells with α-amanitin or actinomycin D revealed that extension of B2 RNA by Pol II destabilizes the RNA. Our studies provide compelling evidence that mammalian Pol II acts as an RdRP to control the stability of a cellular RNA by extending its 3'-end.
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37
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Donghi D, Pechlaner M, Finazzo C, Knobloch B, Sigel RKO. The structural stabilization of the κ three-way junction by Mg(II) represents the first step in the folding of a group II intron. Nucleic Acids Res 2012; 41:2489-504. [PMID: 23275550 PMCID: PMC3575829 DOI: 10.1093/nar/gks1179] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Folding of group II introns is characterized by a first slow compaction of domain 1 (D1) followed by the rapid docking of other domains to this scaffold. D1 compaction initiates in a small subregion encompassing the κ and ζ elements. These two tertiary elements are also the major interaction sites with domain 5 to form the catalytic core. Here, we provide the first characterization of the structure adopted at an early folding step and show that the folding control element can be narrowed down to the three-way junction with the κ motif. In our nuclear magnetic resonance studies of this substructure derived from the yeast mitochondrial group II intron Sc.ai5γ, we show that a high affinity Mg(II) ion stabilizes the κ element and enables coaxial stacking between helices d′ and d′′, favoring a rigid duplex across the three-way junction. The κ-element folds into a stable GAAA-tetraloop motif and engages in A-minor interactions with helix d′. The addition of cobalt(III)hexammine reveals three distinct binding sites. The Mg(II)-promoted structural rearrangement and rigidification of the D1 core can be identified as the first micro-step of D1 folding.
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Affiliation(s)
- Daniela Donghi
- Institute of Inorganic Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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38
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Abstract
This chapter describes the preparation of NMR quantities of RNA purified to single-nucleotide resolution for protein-RNA interaction studies. The protocol is easily modified to make nucleotide-specific isotopically labeled RNAs or uniformly labeled RNA fragments for ligation to generate segmentally labeled RNAs.
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Affiliation(s)
- Carla A Theimer
- Department of Chemistry, University at Albany SUNY, Albany, NY, USA.
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39
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Schwartz A, Rabhi M, Margeat E, Boudvillain M. Analysis of helicase-RNA interactions using nucleotide analog interference mapping. Methods Enzymol 2012; 511:149-69. [PMID: 22713319 DOI: 10.1016/b978-0-12-396546-2.00007-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Nucleotide analog interference mapping (NAIM) is a combinatorial approach that probes individual atoms and functional groups in an RNA molecule and identifies those that are important for a specific biochemical function. Here, we show how NAIM can be adapted to reveal functionally important atoms and groups on RNA substrates of helicases. We explain how NAIM can be used to investigate translocation and unwinding mechanisms of helicases and discuss the advantages and limitations of this powerful chemogenetic approach.
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Affiliation(s)
- Annie Schwartz
- CNRS UPR4301, Centre de Biophysique Moléculaire, Orléans cedex 2, France
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40
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Site-specific fluorescent probing of RNA molecules by unnatural base-pair transcription for local structural conformation analysis. Nat Protoc 2010; 5:1312-23. [DOI: 10.1038/nprot.2010.77] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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41
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The 2'-OH group at the group II intron terminus acts as a proton shuttle. Nat Chem Biol 2010; 6:218-224. [PMID: 20118939 PMCID: PMC2825881 DOI: 10.1038/nchembio.312] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Accepted: 12/17/2009] [Indexed: 11/16/2022]
Abstract
Group II introns are self-splicing ribozymes that excise themselves from precursor RNAs and catalyze the joining of flanking exons. Excised introns can behave as parasitic RNA molecules, catalyzing their own insertion into DNA and RNA via a reverse-splicing reaction. Previous studies have identified mechanistic roles for various functional groups located in the catalytic core of the intron and within target molecules. Here we introduce a new method for synthesizing long RNA molecules with a modified nucleotide at the 3′-terminus. This modification allows us to examine the mechanistic role of functional groups adjacent to the reaction nucleophile. During reverse-splicing, the 3′-OH group of the intron terminus attacks the phosphodiester linkage of spliced exon sequences. Here we show that the adjacent 2′-OH group on the intron terminus plays an essential role in activating the nucleophile by stripping away a proton from the 3′-OH and then shuttling it from the active-site.
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42
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Boudvillain M, Walmacq C, Schwartz A, Jacquinot F. Simple enzymatic assays for the in vitro motor activity of transcription termination factor Rho from Escherichia coli. Methods Mol Biol 2010; 587:137-154. [PMID: 20225147 DOI: 10.1007/978-1-60327-355-8_10] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The transcription termination factor Rho from Escherichia coli is a ring-shaped homo-hexameric protein that preferentially interacts with naked cytosine-rich Rut (Rho utilization) regions of nascent RNA transcripts. Once bound to the RNA chain, Rho uses ATP as an energy source to produce mechanical work and disruptive forces that ultimately lead to the dissociation of the ternary transcription complex. Although transcription termination assays have been useful to study Rho activity in various experimental contexts, they do not report directly on Rho mechanisms and kinetics. Here, we describe complementary ATP-dependent RNA-DNA helicase and streptavidin displacement assays that can be used to monitor in vitro Rho's motor activity in a more direct and quantitative manner.
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Affiliation(s)
- Marc Boudvillain
- Centre de Biophysique Moleculaire (UPR4301), CNRS, Orleans cedex 2, Orleans, France
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43
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Abstract
A number of RNAs ranging from small helices to large megadalton ribonucleoprotein complexes have been solved to atomic resolution using X-ray crystallography. As with proteins, RNA crystallography involves a number of screening trials in which the concentration of macromolecule, precipitant, salt, and temperature are varied, an approach known as searching "condition space." In contrast to proteins, the nature of base pairing in nucleic acids creates predictable secondary structure that facilitates the rational design of RNA variants, allowing "sequence space" to be screened in parallel. This chapter reviews RNA-specific techniques and considerations for RNA crystallography and presents a complete workflow used by our laboratory for solving RNA structures starting with initial library construction, methods to investigate and improve RNA crystal quality, and finally phase determination and structure solution.
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Affiliation(s)
- Francis E Reyes
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado, USA
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44
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Linear group II intron RNAs can retrohome in eukaryotes and may use nonhomologous end-joining for cDNA ligation. Proc Natl Acad Sci U S A 2009; 106:18189-94. [PMID: 19833873 DOI: 10.1073/pnas.0910277106] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mobile group II introns retrohome by an RNP-based mechanism in which the excised intron lariat RNA fully reverse splices into a DNA site via 2 sequential transesterification reactions and is reverse transcribed by the associated intron-encoded protein. However, linear group II intron RNAs, which can arise by either hydrolytic splicing or debranching of lariat RNA, cannot carry out both reverse-splicing steps and were thus expected to be immobile. Here, we used facile microinjection assays in 2 eukaryotic systems, Xenopus laevis oocyte nuclei and Drosophila melanogaster embryos, to show that group II intron RNPs containing linear intron RNA can retrohome by carrying out the first step of reverse splicing into a DNA site, thereby ligating the 3' end of the intron RNA to the 5' end of the downstream exon DNA. The attached linear intron RNA is then reverse transcribed, yielding an intron cDNA whose free end is linked to the upstream exon DNA. Some of these retrohoming events result in the precise insertion of full-length intron. Most, however, yield aberrant 5' junctions with 5' exon resections, 5' intron truncations, and/or extra nucleotide residues, hallmarks of nonhomologous end-joining. Our findings reveal a mobility mechanism for linear group II intron RNAs, show how group II introns can co-opt different DNA repair pathways for retrohoming, and suggest that linear group II intron RNAs might be used for site-specific DNA integration in gene targeting.
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45
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Werner A, Konarev PV, Svergun DI, Hahn U. Characterization of a fluorophore binding RNA aptamer by fluorescence correlation spectroscopy and small angle X-ray scattering. Anal Biochem 2009; 389:52-62. [PMID: 19303859 DOI: 10.1016/j.ab.2009.03.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2009] [Accepted: 03/12/2009] [Indexed: 01/14/2023]
Abstract
Using fluorescence correlation spectroscopy (FCS), we have established an in vitro assay to study RNA dynamics by analyzing fluorophore binding RNA aptamers at the single molecule level. The RNA aptamer SRB2m, a minimized variant of the initially selected aptamer SRB-2, has a high affinity to the disulfonated triphenylmethane dye sulforhodamine B. A mobility shift of sulforhodamine B after binding to SRB2m was measured. In contrast, patent blue V (PBV) is visible only if complexed with SRB2m due to increased molecular brightness and minimal background. With small angle X-ray scattering (SAXS), the three-dimensional structure of the RNA aptamer was characterized at low resolution to analyze the effect of fluorophore binding. The aptamer and sulforhodamine B-aptamer complex was found to be predominantly dimeric in solution. Interaction of PBV with SRB2m led to a dissociation of SRB2m dimers into monomers. Radii of gyration and hydrodynamic radii, gained from dynamic light scattering, FCS, and fluorescence cross-correlation experiments, led to comparable conclusions. Our study demonstrates how RNA-aptamer fluorophore complexes can be simultaneously structurally and photophysically characterized by FCS. Furthermore, fluorophore binding RNA aptamers provide a tool for visualizing single RNA molecules.
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Affiliation(s)
- Arne Werner
- Institute for Biochemistry and Molecular Biology, Department of Chemistry, Faculty of Mathematics, Informatics, and Natural Sciences, Hamburg University, D-20146 Hamburg, Germany
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Roitzsch M, Pyle AM. The linear form of a group II intron catalyzes efficient autocatalytic reverse splicing, establishing a potential for mobility. RNA (NEW YORK, N.Y.) 2009; 15:473-482. [PMID: 19168748 PMCID: PMC2657011 DOI: 10.1261/rna.1392009] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2008] [Accepted: 11/17/2008] [Indexed: 05/27/2023]
Abstract
Self-splicing group II introns catalyze their own excision from pre-RNAs, thereby joining the flanking exons. The introns can be released in a lariat or linear form. Lariat introns have been shown to reverse the splicing reaction; in contrast, linear introns are generally believed to perform no or only poor reverse splicing. Here, we show that a linear group II intron derived from ai5gamma can reverse the second step of splicing with unexpectedly high efficiency and precision. Moreover, the linear intron generates dramatically more reverse-splicing product than its lariat equivalent. The finding that linear group II introns can readily undergo the critical first step of mobility by catalyzing efficient reverse splicing into complementary target molecules demonstrates their innate potential for mobility and transposition and raises the possibility that reverse splicing by linear group II introns may have played a significant role in certain forms of intron mobility and lateral gene transfer during evolution.
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Affiliation(s)
- Michael Roitzsch
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520, USA
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Watrin M, Dausse E, Lebars I, Rayner B, Bugaut A, Toulmé JJ. Aptamers targeting RNA molecules. Methods Mol Biol 2009; 535:79-105. [PMID: 19377979 DOI: 10.1007/978-1-59745-557-2_6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Oligonucleotides complementary to RNA sequences interact poorly with folded target regions. In vitro selection of oligonucleotides carried out against RNA structures have led to aptamers that frequently differ from antisense sequences, but rather take advantage of non-double-stranded peculiarities of the target. Studies along this line provide information about tertiary RNA architectures as well as their interaction with ligand of interest. We describe here a genomic SELEX approach and its application to the recognition of stem-loop structures prone to the formation of kissing complexes. We also provide technical details for running a procedure termed 2D-SELEX that takes advantage of both in vitro selection and dynamic combinatorial chemistry. This allows selecting aptamer derivatives containing modified nucleotides that cannot be incorporated by polymerases. Last we present in vitro transcription conditions under which large amounts of RNA, suitable for NMR structural studies, can be obtained. These different aspects of the SELEX technology have been applied to the trans-activating responsive element of the human immunodeficiency virus type 1, which is crucial for the transcription of the retroviral genome.
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Affiliation(s)
- Marguerite Watrin
- Institut Européen de Chimie et Biologie, Pessac, France, Université Victor Segalen, Bordeaux, France
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48
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Phosphoserine aminoacylation of tRNA bearing an unnatural base anticodon. Biochem Biophys Res Commun 2008; 372:480-5. [DOI: 10.1016/j.bbrc.2008.05.078] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2008] [Accepted: 05/15/2008] [Indexed: 11/23/2022]
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49
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Veedu RN, Vester B, Wengel J. Polymerase chain reaction and transcription using locked nucleic acid nucleotide triphosphates. J Am Chem Soc 2008; 130:8124-5. [PMID: 18533656 DOI: 10.1021/ja801389n] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Polymerase chain reaction amplification of a locked nucleic acid (LNA)-modified DNA strand and transcription reactions using LNA-A nucleoside 5'-triphosphate were successfully accomplished with DNA and RNA polymerases.
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Affiliation(s)
- Rakesh N Veedu
- Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, Odense M, 5230, Denmark
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50
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Kimoto M, Mitsui T, Harada Y, Sato A, Yokoyama S, Hirao I. Fluorescent probing for RNA molecules by an unnatural base-pair system. Nucleic Acids Res 2007; 35:5360-9. [PMID: 17693436 PMCID: PMC2018647 DOI: 10.1093/nar/gkm508] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Fluorescent labeling of nucleic acids is widely used in basic research and medical applications. We describe the efficient site-specific incorporation of a fluorescent base analog, 2-amino-6-(2-thienyl)purine (s), into RNA by transcription mediated by an unnatural base pair between s and pyrrole-2-carbaldehyde (Pa). The ribonucleoside 5′-triphosphate of s was site-specifically incorporated into RNA, by T7 RNA polymerase, opposite Pa in DNA templates. The fluorescent intensity of s in RNA molecules changes according to the structural environment. The site-specific s labeling of RNA hairpins and tRNA molecules provided characteristic fluorescent profiles, depending on the labeling sites, temperature and Mg2+ concentration. The Pa-containing DNA templates can be amplified by PCR using 7-(2-thienyl)imidazo[4,5-b]pyridine (Ds), another pairing partner of Pa. This site-specific fluorescent probing by the unnatural pair system including the s-Pa and Ds-Pa pairs provides a powerful tool for studying the dynamics of the local structural features of 3D RNA molecules and their intra- and intermolecular interactions.
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Affiliation(s)
- Michiko Kimoto
- Protein Research Group, RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, and RIKEN Harima Institute at SPring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo, Hyogo 679-5148, Japan
| | - Tsuneo Mitsui
- Protein Research Group, RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, and RIKEN Harima Institute at SPring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo, Hyogo 679-5148, Japan
| | - Yoko Harada
- Protein Research Group, RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, and RIKEN Harima Institute at SPring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo, Hyogo 679-5148, Japan
| | - Akira Sato
- Protein Research Group, RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, and RIKEN Harima Institute at SPring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo, Hyogo 679-5148, Japan
| | - Shigeyuki Yokoyama
- Protein Research Group, RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, and RIKEN Harima Institute at SPring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo, Hyogo 679-5148, Japan
| | - Ichiro Hirao
- Protein Research Group, RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, and RIKEN Harima Institute at SPring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo, Hyogo 679-5148, Japan
- *To whom correspondence should be addressed. +81 45 503 9644+81 45 503 9645
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