1
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Warrier I, Perry A, Hubbell SM, Eichelman M, van Opijnen T, Meyer MM. RNA cis-regulators are important for Streptococcus pneumoniae in vivo success. PLoS Genet 2024; 20:e1011188. [PMID: 38442125 PMCID: PMC10942264 DOI: 10.1371/journal.pgen.1011188] [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: 12/13/2023] [Revised: 03/15/2024] [Accepted: 02/19/2024] [Indexed: 03/07/2024] Open
Abstract
Bacteria have evolved complex transcriptional regulatory networks, as well as many diverse regulatory strategies at the RNA level, to enable more efficient use of metabolic resources and a rapid response to changing conditions. However, most RNA-based regulatory mechanisms are not well conserved across different bacterial species despite controlling genes important for virulence or essential biosynthetic processes. Here, we characterize the activity of, and assess the fitness benefit conferred by, twelve cis-acting regulatory RNAs (including several riboswitches and a T-box), in the opportunistic pathogen Streptococcus pneumoniae TIGR4. By evaluating native locus mutants of each regulator that result in constitutively active or repressed expression, we establish that growth defects in planktonic culture are associated with constitutive repression of gene expression, while constitutive activation of gene expression is rarely deleterious. In contrast, in mouse nasal carriage and pneumonia models, strains with either constitutively active and repressed gene expression are significantly less fit than matched control strains. Furthermore, two RNA-regulated pathways, FMN synthesis/transport and pyrimidine synthesis/transport display exceptional sensitivity to mis-regulation or constitutive gene repression in both planktonic culture and in vivo environments. Thus, despite lack of obvious phenotypes associated with constitutive gene expression in vitro, the fitness benefit conferred on bacteria via fine-tuned metabolic regulation through cis-acting regulatory RNAs is substantial in vivo, and therefore easily sufficient to drive the evolution and maintenance of diverse RNA regulatory mechanisms.
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Affiliation(s)
- Indu Warrier
- Boston College Department of Biology, Chestnut Hill, Massachusetts, United States of America
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America
| | - Ariana Perry
- Boston College Department of Biology, Chestnut Hill, Massachusetts, United States of America
| | - Sara M. Hubbell
- Boston College Department of Biology, Chestnut Hill, Massachusetts, United States of America
| | - Matthew Eichelman
- Boston College Department of Biology, Chestnut Hill, Massachusetts, United States of America
| | - Tim van Opijnen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Boston Children’s Hospital, Division of Infectious Diseases, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Michelle M. Meyer
- Boston College Department of Biology, Chestnut Hill, Massachusetts, United States of America
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2
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Passalacqua LFM, Banco MT, Moon JD, Li X, Jaffrey SR, Ferré-D'Amaré AR. Intricate 3D architecture of a DNA mimic of GFP. Nature 2023; 618:1078-1084. [PMID: 37344591 PMCID: PMC10754392 DOI: 10.1038/s41586-023-06229-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 05/16/2023] [Indexed: 06/23/2023]
Abstract
Numerous studies have shown how RNA molecules can adopt elaborate three-dimensional (3D) architectures1-3. By contrast, whether DNA can self-assemble into complex 3D folds capable of sophisticated biochemistry, independent of protein or RNA partners, has remained mysterious. Lettuce is an in vitro-evolved DNA molecule that binds and activates4 conditional fluorophores derived from GFP. To extend previous structural studies5,6 of fluorogenic RNAs, GFP and other fluorescent proteins7 to DNA, we characterize Lettuce-fluorophore complexes by X-ray crystallography and cryogenic electron microscopy. The results reveal that the 53-nucleotide DNA adopts a four-way junction (4WJ) fold. Instead of the canonical L-shaped or H-shaped structures commonly seen8 in 4WJ RNAs, the four stems of Lettuce form two coaxial stacks that pack co-linearly to form a central G-quadruplex in which the fluorophore binds. This fold is stabilized by stacking, extensive nucleobase hydrogen bonding-including through unusual diagonally stacked bases that bridge successive tiers of the main coaxial stacks of the DNA-and coordination of monovalent and divalent cations. Overall, the structure is more compact than many RNAs of comparable size. Lettuce demonstrates how DNA can form elaborate 3D structures without using RNA-like tertiary interactions and suggests that new principles of nucleic acid organization will be forthcoming from the analysis of complex DNAs.
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Affiliation(s)
- Luiz F M Passalacqua
- Laboratory of Nucleic Acids, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Michael T Banco
- Laboratory of Nucleic Acids, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jared D Moon
- Department of Pharmacology, Weill-Cornell Medical College, Cornell University, New York, NY, USA
| | - Xing Li
- Department of Pharmacology, Weill-Cornell Medical College, Cornell University, New York, NY, USA
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Samie R Jaffrey
- Department of Pharmacology, Weill-Cornell Medical College, Cornell University, New York, NY, USA
| | - Adrian R Ferré-D'Amaré
- Laboratory of Nucleic Acids, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
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3
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Marton Menendez A, Nesbitt DJ. Ionic Cooperativity between Lysine and Potassium in the Lysine Riboswitch: Single-Molecule Kinetic and Thermodynamic Studies. J Phys Chem B 2023; 127:2430-2440. [PMID: 36916791 DOI: 10.1021/acs.jpcb.3c00245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Functionality in many biological systems, including proteins and nucleic acid structures, including protein and nucleic acid riboswitch structures, can depend on cooperative kinetic behavior between multiple small molecule ligands. In this work, single-molecule FRET data on the Bacillus subtilis lysine riboswitch reveals that affinity for the cognate lysine ligand increases significantly with K+, providing evidence for synergism between lysine/K+ binding to the aptamer and successful folding of the riboswitch. To describe/interpret this more complex kinetic scenario, we explore the conventional 4-state ("square") model for aptamer binding as a function of K+. Extension into this additional dimension generates a novel "cube" model for riboswitch folding dynamics with respect to lysine/K+ binding, revealing that riboswitch folding (kfold) and unfolding (kunfold) rate constants increase and decrease dramatically with K+, respectively. Furthermore, temperature-dependent single-molecule kinetic studies indicate that the presence of K+ entropically enhances the transition state barrier to folding but partially compensates for this by increasing the overall exothermicity for lysine binding. We rationalize this behavior as evidence that K+ facilitates hydrogen bonding between the negatively charged carboxyl group of lysine and the RNA, increasing structural rigidity and lowering entropy in the binding pocket. Finally, we explore the effects of cation size with Na+ and Cs+ studies to demonstrate that K+ is optimally suited for bridging interactions between lysine and the riboswitch aptamer domain. Regulation of lysine production and transport, dictated by the riboswitch's ability to recognize and bind lysine, is therefore intimately tied to the presence of K+ in the binding pocket and is strongly modulated by local cation conditions. The results suggest an increase in lysine riboswitch functionality by sensitivity to additional species in the cellular riboswitch environment.
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Affiliation(s)
- Andrea Marton Menendez
- JILA, University of Colorado Boulder and National Institute of Standards and Technology, Boulder, Colorado 80309, United States
- Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - David J Nesbitt
- JILA, University of Colorado Boulder and National Institute of Standards and Technology, Boulder, Colorado 80309, United States
- Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
- Department of Physics, University of Colorado Boulder, Boulder, Colorado 80309, United States
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4
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Lenkeit F, Eckert I, Sinn M, Hauth F, Hartig JS, Weinberg Z. A variant of guanidine-IV riboswitches exhibits evidence of a distinct ligand specificity. RNA Biol 2023; 20:10-19. [PMID: 36548032 PMCID: PMC9788692 DOI: 10.1080/15476286.2022.2160562] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Riboswitches are regulatory RNAs that specifically bind a small molecule or ion. Like metabolite-binding proteins, riboswitches can evolve new ligand specificities, and some examples of this phenomenon have been validated. As part of work based on comparative genomics to discover novel riboswitches, we encountered a candidate riboswitch with striking similarities to the recently identified guanidine-IV riboswitch. This candidate riboswitch, the Gd4v motif, is predicted in four distinct bacterial phyla, thus almost as widespread as the guanidine-IV riboswitch. Bioinformatic and experimental analysis suggest that the Gd4v motif is a riboswitch that binds a ligand other than guanidine. It is found associated with gene classes that differ from genes regulated by confirmed guanidine riboswitches. In inline-probing assays, we showed that free guanidine binds only weakly to one of the tested sequences of the variant. Further tested compounds did not show binding, attenuation of transcription termination, or activation of a genetic reporter construct. We characterized an N-acetyltransferase frequently associated with the Gd4v motif and compared its substrate preference to an N-acetyltransferase that occurs under control of guanidine-IV riboswitches. The substrates of this Gd4v-motif-associated enzyme did not show activity for Gd4v RNA binding or transcription termination. Hence, the ligand of the candidate riboswitch motif remains unidentified. The variant RNA motif is predominantly found in gut metagenome sequences, hinting at a ligand that is highly relevant in this environment. This finding is a first step to determining the identity of this unknown ligand, and understanding how guanidine-IV-riboswitch-like structures can evolve to bind different ligands.
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Affiliation(s)
- Felina Lenkeit
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457Konstanz, Germany
| | - Iris Eckert
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Centre for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107Leipzig, Germany
| | - Malte Sinn
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457Konstanz, Germany
| | - Franziskus Hauth
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457Konstanz, Germany
| | - Jörg S. Hartig
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457Konstanz, Germany,CONTACT Jörg S. Hartig
| | - Zasha Weinberg
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Centre for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107Leipzig, Germany,Zasha Weinberg Bioinformatics Group, Department of Computer Science and Interdisciplinary Centre for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107Leipzig, Germany
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5
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Bonilla SL, Kieft JS. The promise of cryo-EM to explore RNA structural dynamics. J Mol Biol 2022; 434:167802. [PMID: 36049551 PMCID: PMC10084733 DOI: 10.1016/j.jmb.2022.167802] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 08/24/2022] [Accepted: 08/24/2022] [Indexed: 01/13/2023]
Abstract
Conformational dynamics are essential to macromolecular function. This is certainly true of RNA, whose ability to undergo programmed conformational dynamics is essential to create and regulate complex biological processes. However, methods to easily and simultaneously interrogate both the structure and conformational dynamics of fully functional RNAs in isolation and in complex with proteins have not historically been available. Due to its ability to image and classify single particles, cryogenic electron microscopy (cryo-EM) has the potential to address this gap and may be particularly amenable to exploring structural dynamics within the three-dimensional folds of biologically active RNAs. We discuss the possibilities and current limitations of applying cryo-EM to simultaneously study RNA structure and conformational dynamics, and present one example that illustrates this (as of yet) not fully realized potential.
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Affiliation(s)
- Steve L Bonilla
- Department of Biochemistry and Molecular Genetics, Aurora, CO 80045, USA. https://twitter.com/Steve_Bonilla
| | - Jeffrey S Kieft
- Department of Biochemistry and Molecular Genetics, Aurora, CO 80045, USA; RNA BioScience Initiative, University of Colorado Anschutz Medical Campus, School of Medicine, Aurora, CO 80045, USA.
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6
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Manna S, Sontakke VA, Srivatsan SG. Incorporation and Utility of a Responsive Ribonucleoside Analogue in Probing the Conformation of a Viral RNA Motif by Fluorescence and 19 F NMR Spectroscopy. Chembiochem 2021; 23:e202100601. [PMID: 34821449 DOI: 10.1002/cbic.202100601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/24/2021] [Indexed: 11/09/2022]
Abstract
Development of versatile probes that can enable the study of different conformations and recognition properties of therapeutic nucleic acid motifs by complementing biophysical techniques can greatly aid nucleic acid analysis and therapy. Here, we report the design, synthesis and incorporation of an environment-sensitive ribonucleoside analogue, which serves as a two-channel biophysical platform to investigate RNA structure and recognition by fluorescence and 19 F NMR spectroscopy techniques. The nucleoside analogue is based on a 5-fluorobenzofuran-uracil core and its fluorescence and 19 F NMR chemical shifts are highly sensitive to changes in solvent polarity and viscosity. Notably, the modified ribonucleotide and phosphoramidite substrates can be efficiently incorporated into RNA oligonucleotides (ONs) by in vitro transcription and standard solid-phase ON synthesis protocol, respectively. Fluorescence and 19 F readouts of the nucleoside incorporated into model RNA ONs are sensitive to the neighbouring base environment. The responsiveness of the probe was aptly utilized in detecting and quantifying the metal ion-induced conformational change in an internal ribosome entry site RNA motif of hepatitis C virus, which is an important therapeutic target. Taken together, our probe is a good addition to the nucleic acid analysis toolbox with the advantage that it can be used to study nucleic acid conformation and recognition simultaneously by two biophysical techniques.
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Affiliation(s)
- Sudeshna Manna
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road, Pune, 411008, India
| | - Vyankat A Sontakke
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road, Pune, 411008, India
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road, Pune, 411008, India
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7
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Zhang D, Chen SJ, Zhou R. Modeling Noncanonical RNA Base Pairs by a Coarse-Grained IsRNA2 Model. J Phys Chem B 2021; 125:11907-11915. [PMID: 34694128 DOI: 10.1021/acs.jpcb.1c07288] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Noncanonical base pairs contribute crucially to the three-dimensional architecture of large RNA molecules; however, how to accurately model them remains an open challenge in RNA 3D structure prediction. Here, we report a promising coarse-grained (CG) IsRNA2 model to predict noncanonical base pairs in large RNAs through molecular dynamics simulations. By introducing a five-bead per nucleotide CG representation to reserve the three interacting edges of nucleobases, IsRNA2 accurately models various base-pairing interactions, including both canonical and noncanonical base pairs. A benchmark test indicated that IsRNA2 achieves a comparable performance to the atomic model in de novo modeling of noncanonical RNA structures. In addition, IsRNA2 was able to refine the 3D structure predictions for large RNAs in RNA-puzzle challenges. Finally, the graphics processing unit acceleration was introduced to speed up the sampling efficiency in IsRNA2 for very large RNA molecules. Therefore, the CG IsRNA2 model reported here offers a reliable approach to predict the structures and dynamics of large RNAs.
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Affiliation(s)
- Dong Zhang
- College of Life Sciences and Institute of Quantitative Biology, Zhejiang University, Hangzhou 310058, China
| | - Shi-Jie Chen
- Department of Physics, Department of Biochemistry, and Institute of Data Science and Informatics, University of Missouri, Columbia, Missouri 65211, United States
| | - Ruhong Zhou
- College of Life Sciences and Institute of Quantitative Biology, Zhejiang University, Hangzhou 310058, China
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8
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Flemmich L, Heel S, Moreno S, Breuker K, Micura R. A natural riboswitch scaffold with self-methylation activity. Nat Commun 2021; 12:3877. [PMID: 34162884 PMCID: PMC8222354 DOI: 10.1038/s41467-021-24193-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 06/04/2021] [Indexed: 11/12/2022] Open
Abstract
Methylation is a prevalent post-transcriptional modification encountered in coding and non-coding RNA. For RNA methylation, cells use methyltransferases and small organic substances as methyl-group donors, such as S-adenosylmethionine (SAM). SAM and other nucleotide-derived cofactors are viewed as evolutionary leftovers from an RNA world, in which riboswitches have regulated, and ribozymes have catalyzed essential metabolic reactions. Here, we disclose the thus far unrecognized direct link between a present-day riboswitch and its inherent reactivity for site-specific methylation. The key is O6-methyl pre-queuosine (m6preQ1), a potentially prebiotic nucleobase which is recognized by the native aptamer of a preQ1 class I riboswitch. Upon binding, the transfer of the ligand’s methyl group to a specific cytidine occurs, installing 3-methylcytidine (m3C) in the RNA pocket under release of pre-queuosine (preQ1). Our finding suggests that nucleic acid-mediated methylation is an ancient mechanism that has offered an early path for RNA epigenetics prior to the evolution of protein methyltransferases. Furthermore, our findings may pave the way for the development of riboswitch-descending methylation tools based on rational design as a powerful alternative to in vitro selection approaches. In humans, protein methyltransferase is responsible for RNA methylation using S-adenosylmethionine as a methyl group donor. Here the authors report a self-methylation activity of a bacterial riboswitch.
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Affiliation(s)
- Laurin Flemmich
- University of Innsbruck, Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), Innrain 80-82, Innsbruck, 6020, Austria
| | - Sarah Heel
- University of Innsbruck, Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), Innrain 80-82, Innsbruck, 6020, Austria
| | - Sarah Moreno
- University of Innsbruck, Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), Innrain 80-82, Innsbruck, 6020, Austria
| | - Kathrin Breuker
- University of Innsbruck, Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), Innrain 80-82, Innsbruck, 6020, Austria
| | - Ronald Micura
- University of Innsbruck, Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), Innrain 80-82, Innsbruck, 6020, Austria.
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9
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Nuthanakanti A, Srivatsan SG. Synthesis of DNA and RNA Oligonucleotides Containing a Dual-Purpose Selenium-Modified Fluorescent Nucleoside Probe. ACTA ACUST UNITED AC 2021; 81:e106. [PMID: 32311240 DOI: 10.1002/cpnc.106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Development of efficient tools that would enable direct correlation of nucleic acid structure and recognition in solution and in solid state at atomic resolution is highly desired. In this context, we recently developed dual-purpose nucleoside probes made of a 5-selenophene-modified uracil core, which serves both as a conformation-sensitive fluorophore and as an X-ray crystallography phasing agent. In this article, we provide a detailed synthetic procedure to synthesize the phosphoramidites of 5-selenophene-modified 2'-deoxyuridine and 5-selenophene-modified uridine analogs. We also describe their site-specific incorporation into therapeutically relevant DNA and RNA oligonucleotide motifs by an automated solid support synthesis protocol. The dual-purpose and minimally invasive nature of the probes enables efficient analysis of the conformation and ligand binding abilities of bacterial decoding site RNA (A-site) and G-quadruplex structures of the human telomeric overhang in real time by fluorescence and in 3D by X-ray crystallography. © 2020 by John Wiley & Sons, Inc. Basic Protocol 1: Synthesis of 5-selenophene-2'-deoxyuridine 2 and its phosphoramidite 5 Support Protocol 1: Synthesis of 2-(tri-n-butylstannyl) selenophene Support Protocol 2: Synthesis of 5'-O-DMT-protected 5-iodo-2'-deoxyuridine 3 Basic Protocol 2: Synthesis of 5-selenophene-modified uridine 7 and its phosphoramidite 11 Basic Protocol 3: Synthesis of DNA oligonucleotides containing 5-selenophene-modified 2'-deoxyuridine 2 Basic Protocol 4: Synthesis of an RNA oligonucleotide containing 5-selenophene-modified uridine 7.
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Affiliation(s)
- Ashok Nuthanakanti
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, India
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, India
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10
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Abdelsattar AS, Mansour Y, Aboul-Ela F. The Perturbed Free-Energy Landscape: Linking Ligand Binding to Biomolecular Folding. Chembiochem 2021; 22:1499-1516. [PMID: 33351206 DOI: 10.1002/cbic.202000695] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/19/2020] [Indexed: 12/24/2022]
Abstract
The effects of ligand binding on biomolecular conformation are crucial in drug design, enzyme mechanisms, the regulation of gene expression, and other biological processes. Descriptive models such as "lock and key", "induced fit", and "conformation selection" are common ways to interpret such interactions. Another historical model, linked equilibria, proposes that the free-energy landscape (FEL) is perturbed by the addition of ligand binding energy for the bound population of biomolecules. This principle leads to a unified, quantitative theory of ligand-induced conformation change, building upon the FEL concept. We call the map of binding free energy over biomolecular conformational space the "binding affinity landscape" (BAL). The perturbed FEL predicts/explains ligand-induced conformational changes conforming to all common descriptive models. We review recent experimental and computational studies that exemplify the perturbed FEL, with emphasis on RNA. This way of understanding ligand-induced conformation dynamics motivates new experimental and theoretical approaches to ligand design, structural biology and systems biology.
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Affiliation(s)
- Abdallah S Abdelsattar
- Center for X-Ray Determination of the Structure of Matter, Zewail City of Science and Technology, Ahmed Zewail Road, October Gardens, 12578, Giza, Egypt
| | - Youssef Mansour
- Center for X-Ray Determination of the Structure of Matter, Zewail City of Science and Technology, Ahmed Zewail Road, October Gardens, 12578, Giza, Egypt
| | - Fareed Aboul-Ela
- Center for X-Ray Determination of the Structure of Matter, Zewail City of Science and Technology, Ahmed Zewail Road, October Gardens, 12578, Giza, Egypt
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11
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Zhang D, Li J, Chen SJ. IsRNA1: De Novo Prediction and Blind Screening of RNA 3D Structures. J Chem Theory Comput 2021; 17:1842-1857. [PMID: 33560836 DOI: 10.1021/acs.jctc.0c01148] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Modeling structures and functions of large ribonucleic acid (RNAs) especially with complicated topologies is highly challenging due to the inefficiency of large conformational sampling and the presence of complicated tertiary interactions. To address this problem, one highly promising approach is coarse-grained modeling. Here, following an iterative simulated reference state approach to decipher the correlations between different structural parameters, we developed a potent coarse-grained RNA model named as IsRNA1 for RNA studies. Molecular dynamics simulations in the IsRNA1 can predict the native structures of small RNAs from a sequence and fold medium-sized RNAs into near-native tertiary structures with the assistance of secondary structure constraints. A large-scale benchmark test on RNA 3D structure prediction shows that IsRNA1 exhibits improved performance for relatively large RNAs of complicated topologies, such as large stem-loop structures and structures containing long-range tertiary interactions. The advantages of IsRNA1 include the consideration of the correlations between the different structural variables, the appropriate characterization of canonical base-pairing and base-stacking interactions, and the better sampling for the backbone conformations. Moreover, a blind screening protocol was developed based on IsRNA1 to identify good structural models from a pool of candidates without prior knowledge of the native structures.
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Affiliation(s)
- Dong Zhang
- Department of Physics, Department of Biochemistry, and Institute of Data Science and Informatics, University of Missouri, Columbia, Missouri 65211, United States
| | - Jun Li
- Department of Physics, Department of Biochemistry, and Institute of Data Science and Informatics, University of Missouri, Columbia, Missouri 65211, United States
| | - Shi-Jie Chen
- Department of Physics, Department of Biochemistry, and Institute of Data Science and Informatics, University of Missouri, Columbia, Missouri 65211, United States
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12
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Hurst T, Zhang D, Zhou Y, Chen SJ. A Bayes-inspired theory for optimally building an efficient coarse-grained folding force field. COMMUNICATIONS IN INFORMATION AND SYSTEMS 2021; 21:65-83. [PMID: 34354546 PMCID: PMC8336718 DOI: 10.4310/cis.2021.v21.n1.a4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Because of their potential utility in predicting conformational changes and assessing folding dynamics, coarse-grained (CG) RNA folding models are appealing for rapid characterization of RNA molecules. Previously, we reported the iterative simulated RNA reference state (IsRNA) method for parameterizing a CG force field for RNA folding, which consecutively updates the simulation force field to reflect marginal distributions of folding coordinates in the structure database and extract various energy terms. While the IsRNA model was validated by showing close agreement between the IsRNA-simulated and experimentally observed distributions, here, we expand our theoretical understanding of the model and, in doing so, improve the parameterization process to optimize the subset of included folding coordinates, which leads to accelerated simulations. Using statistical mechanical theory, we analyze the underlying, Bayesian concept that drives parameterization of the energy function, providing a general method for developing predictive, knowledge-based, polymer force fields on the basis of limited data. Furthermore, we propose an optimal parameterization procedure, based on the principal of maximum entropy.
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Affiliation(s)
- Travis Hurst
- Department of Physics, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - Dong Zhang
- Department of Physics, University of Missouri-Columbia
| | - Yuanzhe Zhou
- Department of Physics, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - Shi-Jie Chen
- Department of Physics, Department of Biochemistry, MU Institute for Data Science and Informatics, University of Missouri-Columbia, Columbia, MO 65211, USA
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13
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Micura R, Höbartner C. Fundamental studies of functional nucleic acids: aptamers, riboswitches, ribozymes and DNAzymes. Chem Soc Rev 2020; 49:7331-7353. [PMID: 32944725 DOI: 10.1039/d0cs00617c] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This review aims at juxtaposing common versus distinct structural and functional strategies that are applied by aptamers, riboswitches, and ribozymes/DNAzymes. Focusing on recently discovered systems, we begin our analysis with small-molecule binding aptamers, with emphasis on in vitro-selected fluorogenic RNA aptamers and their different modes of ligand binding and fluorescence activation. Fundamental insights are much needed to advance RNA imaging probes for detection of exo- and endogenous RNA and for RNA process tracking. Secondly, we discuss the latest gene expression-regulating mRNA riboswitches that respond to the alarmone ppGpp, to PRPP, to NAD+, to adenosine and cytidine diphosphates, and to precursors of thiamine biosynthesis (HMP-PP), and we outline new subclasses of SAM and tetrahydrofolate-binding RNA regulators. Many riboswitches bind protein enzyme cofactors that, in principle, can catalyse a chemical reaction. For RNA, however, only one system (glmS ribozyme) has been identified in Nature thus far that utilizes a small molecule - glucosamine-6-phosphate - to participate directly in reaction catalysis (phosphodiester cleavage). We wonder why that is the case and what is to be done to reveal such likely existing cellular activities that could be more diverse than currently imagined. Thirdly, this brings us to the four latest small nucleolytic ribozymes termed twister, twister-sister, pistol, and hatchet as well as to in vitro selected DNA and RNA enzymes that promote new chemistry, mainly by exploiting their ability for RNA labelling and nucleoside modification recognition. Enormous progress in understanding the strategies of nucleic acids catalysts has been made by providing thorough structural fundaments (e.g. first structure of a DNAzyme, structures of ribozyme transition state mimics) in combination with functional assays and atomic mutagenesis.
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Affiliation(s)
- Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck CMBI, Leopold-Franzens University Innsbruck, Innsbruck, Austria.
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14
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Chan CW, Mondragón A. Crystal structure of an atypical cobalamin riboswitch reveals RNA structural adaptability as basis for promiscuous ligand binding. Nucleic Acids Res 2020; 48:7569-7583. [PMID: 32544228 PMCID: PMC7367189 DOI: 10.1093/nar/gkaa507] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/15/2020] [Accepted: 06/11/2020] [Indexed: 11/25/2022] Open
Abstract
Cobalamin riboswitches encompass a structurally diverse group of cis-acting, gene regulatory elements found mostly in bacterial messenger RNA and are classified into subtypes based on secondary and tertiary characteristics. An unusual variant of the cobalamin riboswitch with predicted structural features was identified in Bacillus subtilis over a decade ago, but its structure and mechanisms of cobalamin selectivity and translational control have remained unsolved. We present the crystal structure of the aptamer domain of this atypical cobalamin riboswitch and a model for the complete riboswitch, including its expression platform domain. We demonstrate that this riboswitch binds to multiple cobalamin derivatives and correlate its promiscuous behavior to its structure and unique arrangement of peripheral elements. Comparative structural analyses between conventional cobalamin riboswitches and the B. subtilis cobalamin riboswitch reveal that the likely basis for this promiscuous ligand binding is intrinsic structural adaptability encoded in the RNA structure. It suggests that cobalamin selectivity might ultimately be viewed as existing on a spectrum of affinity for each derivative rather than as belonging to distinct types based on ligand specificities. Our work provides an interesting and notable example of functional coupling of ligand-sensing and adaptive folding by a structured RNA molecule.
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Affiliation(s)
- Clarence W Chan
- Department of Molecular Biosciences, Northwestern University, 2205 Tech Drive, Evanston, IL 60208-3500, USA
| | - Alfonso Mondragón
- Department of Molecular Biosciences, Northwestern University, 2205 Tech Drive, Evanston, IL 60208-3500, USA
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15
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Tumor Cell-Intrinsic Immunometabolism and Precision Nutrition in Cancer Immunotherapy. Cancers (Basel) 2020; 12:cancers12071757. [PMID: 32630618 PMCID: PMC7409312 DOI: 10.3390/cancers12071757] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 06/26/2020] [Accepted: 06/30/2020] [Indexed: 12/19/2022] Open
Abstract
One of the greatest challenges in the cancer immunotherapy field is the need to biologically rationalize and broaden the clinical utility of immune checkpoint inhibitors (ICIs). The balance between metabolism and immune response has critical implications for overcoming the major weaknesses of ICIs, including their lack of universality and durability. The last decade has seen tremendous advances in understanding how the immune system's ability to kill tumor cells requires the conspicuous metabolic specialization of T-cells. We have learned that cancer cell-associated metabolic activities trigger shifts in the abundance of some metabolites with immunosuppressory roles in the tumor microenvironment. Yet very little is known about the tumor cell-intrinsic metabolic traits that control the immune checkpoint contexture in cancer cells. Likewise, we lack a comprehensive understanding of how systemic metabolic perturbations in response to dietary interventions can reprogram the immune checkpoint landscape of tumor cells. We here review state-of-the-art molecular- and functional-level interrogation approaches to uncover how cell-autonomous metabolic traits and diet-mediated changes in nutrient availability and utilization might delineate new cancer cell-intrinsic metabolic dependencies of tumor immunogenicity. We propose that clinical monitoring and in-depth molecular evaluation of the cancer cell-intrinsic metabolic traits involved in primary, adaptive, and acquired resistance to cancer immunotherapy can provide the basis for improvements in therapeutic responses to ICIs. Overall, these approaches might guide the use of metabolic therapeutics and dietary approaches as novel strategies to broaden the spectrum of cancer patients and indications that can be effectively treated with ICI-based cancer immunotherapy.
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16
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Nuthanakanti A, Ahmed I, Khatik SY, Saikrishnan K, Srivatsan SG. Probing G-quadruplex topologies and recognition concurrently in real time and 3D using a dual-app nucleoside probe. Nucleic Acids Res 2020; 47:6059-6072. [PMID: 31106340 PMCID: PMC6614846 DOI: 10.1093/nar/gkz419] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 04/30/2019] [Accepted: 05/06/2019] [Indexed: 12/30/2022] Open
Abstract
Comprehensive understanding of structure and recognition properties of regulatory nucleic acid elements in real time and atomic level is highly important to devise efficient therapeutic strategies. Here, we report the establishment of an innovative biophysical platform using a dual-app nucleoside analog, which serves as a common probe to detect and correlate different GQ structures and ligand binding under equilibrium conditions and in 3D by fluorescence and X-ray crystallography techniques. The probe (SedU) is composed of a microenvironment-sensitive fluorophore and an excellent anomalous X-ray scatterer (Se), which is assembled by attaching a selenophene ring at 5-position of 2'-deoxyuridine. SedU incorporated into the loop region of human telomeric DNA repeat fluorescently distinguished subtle differences in GQ topologies and enabled quantify ligand binding to different topologies. Importantly, anomalous X-ray dispersion signal from Se could be used to determine the structure of GQs. As the probe is minimally perturbing, a direct comparison of fluorescence data and crystal structures provided structural insights on how the probe senses different GQ conformations without affecting the native fold. Taken together, our dual-app probe represents a new class of tool that opens up new experimental strategies to concurrently investigate nucleic acid structure and recognition in real time and 3D.
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Affiliation(s)
- Ashok Nuthanakanti
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
| | - Ishtiyaq Ahmed
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
| | - Saddam Y Khatik
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
| | - Kayarat Saikrishnan
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
- Correspondence may also be addressed to Kayarat Saikrishnan.
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
- To whom correspondence should be addressed. Tel: +91 2025908086;
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17
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Folding intermediate states of the parallel human telomeric G-quadruplex DNA explored using Well-Tempered Metadynamics. Sci Rep 2020; 10:3176. [PMID: 32081872 PMCID: PMC7035250 DOI: 10.1038/s41598-020-59774-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 01/30/2020] [Indexed: 11/16/2022] Open
Abstract
An increasingly comprehension of the folding intermediate states of DNA G-quadruplexes (G4s) is currently an important scientific challenge, especially for the human telomeric (h-tel) G4s-forming sequences, characterized by a highly polymorphic nature. Despite the G-triplex conformation was proposed as one of the possible folding intermediates for the antiparallel and hybrid h-tel G4s, for the parallel h-tel topology with an all-anti guanine orientation, a vertical strand-slippage involving the G-triplets was proposed in previous works through microseconds-long standard molecular dynamics simulations (MDs). Here, in order to get further insights into the vertical strand-slippage and the folding intermediate states of the parallel h-tel G4s, we have carried out a Well-Tempered Metadynamics simulation (WT-MetaD), which allowed us to retrieve an ensemble of six G4s having two/G-tetrad conformations derived by the G-triplets vertical slippage. The insights highlighted in this work are aimed at rationalizing the mechanistic characterisation of the parallel h-tel G4 folding process.
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18
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Matsumoto S, Caliskan N, Rodnina MV, Murata A, Nakatani K. Small synthetic molecule-stabilized RNA pseudoknot as an activator for -1 ribosomal frameshifting. Nucleic Acids Res 2019; 46:8079-8089. [PMID: 30085309 PMCID: PMC6144811 DOI: 10.1093/nar/gky689] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 07/31/2018] [Indexed: 12/02/2022] Open
Abstract
Programmed –1 ribosomal frameshifting (−1PRF) is a recoding mechanism to make alternative proteins from a single mRNA transcript. −1PRF is stimulated by cis-acting signals in mRNA, a seven-nucleotide slippery sequence and a downstream secondary structure element, which is often a pseudoknot. In this study we engineered the frameshifting pseudoknot from the mouse mammary tumor virus to respond to a rationally designed small molecule naphthyridine carbamate tetramer (NCTn). We demonstrate that NCTn can stabilize the pseudoknot structure in mRNA and activate –1PRF both in vitro and in human cells. The results illustrate how NCTn-inducible –1PRF may serve as an important component of the synthetic biology toolbox for the precise control of gene expression using small synthetic molecules.
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Affiliation(s)
- Saki Matsumoto
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (ISIR), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Neva Caliskan
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research, Josef-Schneider-Str.2/D15, 97080, Würzburg, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Asako Murata
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (ISIR), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (ISIR), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
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19
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Abstract
The three-dimensional structures of RNA molecules provide rich and often critical information for understanding their functions, including how they recognize small molecule and protein partners. Computational modeling of RNA 3D structure is becoming increasingly accurate, particularly with the availability of growing numbers of template structures already solved experimentally and the development of sequence alignment and 3D modeling tools to take advantage of this database. For several recent "RNA puzzle" blind modeling challenges, we have successfully identified useful template structures and achieved accurate structure predictions through homology modeling tools developed in the Rosetta software suite. We describe our semi-automated methodology here and walk through two illustrative examples: an adenine riboswitch aptamer, modeled from a template guanine riboswitch structure, and a SAM I/IV riboswitch aptamer, modeled from a template SAM I riboswitch structure.
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Affiliation(s)
- Andrew M Watkins
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, United States
| | - Ramya Rangan
- Biophysics Program, Stanford University, Stanford, CA, United States
| | - Rhiju Das
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, United States; Biophysics Program, Stanford University, Stanford, CA, United States.
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20
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Rinschen MM, Ivanisevic J, Giera M, Siuzdak G. Identification of bioactive metabolites using activity metabolomics. Nat Rev Mol Cell Biol 2019; 20:353-367. [PMID: 30814649 PMCID: PMC6613555 DOI: 10.1038/s41580-019-0108-4] [Citation(s) in RCA: 552] [Impact Index Per Article: 110.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The metabolome, the collection of small-molecule chemical entities involved in metabolism, has traditionally been studied with the aim of identifying biomarkers in the diagnosis and prediction of disease. However, the value of metabolome analysis (metabolomics) has been redefined from a simple biomarker identification tool to a technology for the discovery of active drivers of biological processes. It is now clear that the metabolome affects cellular physiology through modulation of other 'omics' levels, including the genome, epigenome, transcriptome and proteome. In this Review, we focus on recent progress in using metabolomics to understand how the metabolome influences other omics and, by extension, to reveal the active role of metabolites in physiology and disease. This concept of utilizing metabolomics to perform activity screens to identify biologically active metabolites - which we term activity metabolomics - is already having a broad impact on biology.
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Affiliation(s)
- Markus M Rinschen
- The Scripps Research Institute, Center for Metabolomics and Mass Spectrometry, La Jolla, CA, USA
| | - Julijana Ivanisevic
- Metabolomics Platform, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Martin Giera
- Leiden University Medical Center, Center for Proteomics & Metabolomics, Leiden, Netherlands.
| | - Gary Siuzdak
- The Scripps Research Institute, Center for Metabolomics and Mass Spectrometry, La Jolla, CA, USA.
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21
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Endoh T, Sugimoto N. Co-Transcriptional Molecular Assembly Results in a Kinetically Controlled Irreversible RNA Conformational Switch. Anal Chem 2018; 90:11193-11197. [DOI: 10.1021/acs.analchem.8b03427] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Tamaki Endoh
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi,
Chuo-ku, Kobe, 650-0047, Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi,
Chuo-ku, Kobe, 650-0047, Japan
- Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe, 650-0047, Japan
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22
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Abduljalil JM. Bacterial riboswitches and RNA thermometers: Nature and contributions to pathogenesis. Noncoding RNA Res 2018; 3:54-63. [PMID: 30159440 PMCID: PMC6096418 DOI: 10.1016/j.ncrna.2018.04.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 04/10/2018] [Accepted: 04/10/2018] [Indexed: 12/31/2022] Open
Abstract
Bacterial pathogens are always challenged by fluctuations of chemical and physical parameters that pose serious threats to cellular integrity and metabolic status. Sudden deprivation of nutrients or key metabolites, changes in surrounding pH, and temperature shifts are the most important examples of such parameters. To elicit a proper response to such fluctuations, bacterial cells coordinate the expression of parameter-relevant genes. Although protein-mediated control of gene expression is well appreciated since many decades, RNA-based regulation has been discovered in early 2000s as a parallel level of regulation. Small regulatory RNAs have emerged as one of the most widespread and important gene regulatory systems in bacteria with rare representatives found in Archaea and Eukarya. Riboswitches and thermosensors are cis-encoded RNA regulatory elements that employ different mechanisms to regulate the expression of related genes controlling key metabolic pathways and genes of temperature relevant proteins including virulence factors. The extent of RNA contributions to gene regulation is not completely known even in well-studied models such E. coli and B. subtilis. In depth understanding of riboswitches is promising for opportunity to discover a narrow spectrum antibacterial drugs that target riboswitches of essential metabolic pathways.
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Key Words
- 5ʹ-UTRs, 5ʹ-untranslated region
- AdoCbl, adenosylcobalamine
- Aptamer
- Bacterial pathogenicity
- CSPs, Cold Shock Proteins
- FMN, Flavin mononucleotide
- Gene expression
- ORFs, open reading frames
- RBS, Ribosomal Binding Site
- RNA thermometer
- RNAP, RNA polymerase
- RNAT, RNA thermometer
- Riboswitches
- SAH, S-adenosylhomocysteine
- SAM, S-adenosylmethionine
- SD, Shine-Dalgarno
- TPP, Thiamine pyrophosphate
- Transcription termination
- Virulence
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23
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Efficient computation of co-transcriptional RNA-ligand interaction dynamics. Methods 2018; 143:70-76. [PMID: 29730250 DOI: 10.1016/j.ymeth.2018.04.036] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 04/26/2018] [Accepted: 04/29/2018] [Indexed: 11/23/2022] Open
Abstract
Riboswitches form an abundant class of cis-regulatory RNA elements that mediate gene expression by binding a small metabolite. For synthetic biology applications, they are becoming cheap and accessible systems for selectively triggering transcription or translation of downstream genes. Many riboswitches are kinetically controlled, hence knowledge of their co-transcriptional mechanisms is essential. We present here an efficient implementation for analyzing co-transcriptional RNA-ligand interaction dynamics. This approach allows for the first time to model concentration-dependent metabolite binding/unbinding kinetics. We exemplify this novel approach by means of the recently studied I-A 2'-deoxyguanosine (2'dG)-sensing riboswitch from Mesoplasma florum.
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24
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Zhang D, Chen SJ. IsRNA: An Iterative Simulated Reference State Approach to Modeling Correlated Interactions in RNA Folding. J Chem Theory Comput 2018; 14:2230-2239. [PMID: 29499114 DOI: 10.1021/acs.jctc.7b01228] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Coarse-grained RNA folding models promise great potential for RNA structure prediction. A key component in a coarse-grained folding model is the force field. One of the challenges in the coarse-grained force field calculation is how to treat the correlation between the different degrees of freedoms. Here, we describe a new approach (IsRNA) to extract the correlated energy functions from the known structures. Through iterative molecular dynamics simulations, we build the correlation effects into the reference states, from which we extract the energy functions. The validity of IsRNA is supported by the close agreement between the simulated Boltzmann-like probability distributions for all the structure parameters and those observed from the experimentally determined structures. The correlated energy functions derived here may provide a new tool for RNA 3D structure prediction.
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Affiliation(s)
- Dong Zhang
- Department of Physics, Department of Biochemistry, and MU Informatics Institute , University of Missouri , Columbia , Missouri 65211 , United States
| | - Shi-Jie Chen
- Department of Physics, Department of Biochemistry, and MU Informatics Institute , University of Missouri , Columbia , Missouri 65211 , United States
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25
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Schneider C, Bronstein L, Diemer J, Koeppl H, Suess B. ROC'n'Ribo: Characterizing a Riboswitching Expression System by Modeling Single-Cell Data. ACS Synth Biol 2017; 6:1211-1224. [PMID: 28591515 DOI: 10.1021/acssynbio.6b00322] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
RNA-engineered systems offer simple and versatile control over gene expression in many organisms. In particular, the design and implementation of riboswitches presents a unique opportunity to manipulate any reporter device in cis, executing tight temporal and spatial control at low metabolic costs. Assembled to higher order genetic circuits, such riboswitch-regulated devices may efficiently process logical operations. Here, we propose a hierarchical stochastic modeling approach to characterize an in silico repressor gate based on neomycin- and tetracycline-sensitive riboswitches. The model was calibrated on rich, transient in vivo single-cell data to account for cell-to-cell variability. To capture the effect of this variability on gate performance we employed the well-known ROC-analysis and derived a novel performance indicator for logic gates. Introduction of such a performance measure is necessary, since we aimed to assess the correct functionality of the gate at the single-cell level-a prerequisite for its further adaption to a genetic circuitry. Our results may be applied to other genetic devices to analyze their efficiency and ensure their correct performance in the light of cell-to-cell variability.
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Affiliation(s)
- Christopher Schneider
- Department
of Biology, Synthetic Genetic Circuits, TU Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Leo Bronstein
- Department
of Electrical Engineering and Information Technology, Bioinspired
Communications, TU Darmstadt, Rundeturmstrasse 12, 64283 Darmstadt, Germany
| | - Jascha Diemer
- Department
of Electrical Engineering and Information Technology, Bioinspired
Communications, TU Darmstadt, Rundeturmstrasse 12, 64283 Darmstadt, Germany
| | - Heinz Koeppl
- Department
of Electrical Engineering and Information Technology, Bioinspired
Communications, TU Darmstadt, Rundeturmstrasse 12, 64283 Darmstadt, Germany
| | - Beatrix Suess
- Department
of Biology, Synthetic Genetic Circuits, TU Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
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26
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Gong S, Wang Y, Wang Z, Zhang W. Co-Transcriptional Folding and Regulation Mechanisms of Riboswitches. Molecules 2017; 22:molecules22071169. [PMID: 28703767 PMCID: PMC6152003 DOI: 10.3390/molecules22071169] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Revised: 07/07/2017] [Accepted: 07/09/2017] [Indexed: 11/16/2022] Open
Abstract
Riboswitches are genetic control elements within non-coding regions of mRNA. These self-regulatory elements have been found to sense a range of small metabolites, ions, and other physical signals to exert regulatory control of transcription, translation, and splicing. To date, more than a dozen riboswitch classes have been characterized that vary widely in size and secondary structure. Extensive experiments and theoretical studies have made great strides in understanding the general structures, genetic mechanisms, and regulatory activities of individual riboswitches. As the ligand-dependent co-transcriptional folding and unfolding dynamics of riboswitches are the key determinant of gene expression, it is important to investigate the thermodynamics and kinetics of riboswitches both in the presence and absence of metabolites under the transcription. This review will provide a brief summary of the studies about the regulation mechanisms of the pbuE, SMK, yitJ, and metF riboswitches based on the ligand-dependent co-transcriptional folding of the riboswitches.
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Affiliation(s)
- Sha Gong
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang 438000, Hubei, China.
| | - Yanli Wang
- Department of Physics, Wuhan University, Wuhan 430072, Hubei, China.
| | - Zhen Wang
- Department of Physics, Wuhan University, Wuhan 430072, Hubei, China.
| | - Wenbing Zhang
- Department of Physics, Wuhan University, Wuhan 430072, Hubei, China.
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27
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Fresco JR, Amosova O. Site-Specific Self-Catalyzed DNA Depurination: A Biological Mechanism That Leads to Mutations and Creates Sequence Diversity. Annu Rev Biochem 2017; 86:461-484. [PMID: 28654322 DOI: 10.1146/annurev-biochem-070611-095951] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Self-catalyzed DNA depurination is a sequence-specific physiological mechanism mediated by spontaneous extrusion of a stem-loop catalytic intermediate. Hydrolysis of the 5'G residue of the 5'GA/TGG loop and of the first 5'A residue of the 5'GAGA loop, together with particular first stem base pairs, specifies their hydrolysis without involving protein, cofactor, or cation. As such, this mechanism is the only known DNA catalytic activity exploited by nature. The consensus sequences for self-depurination of such G- and A-loop residues occur in all genomes examined across the phyla, averaging one site every 2,000-4,000 base pairs. Because apurinic sites are subject to error-prone repair, leading to substitution and short frameshift mutations, they are both a source of genome damage and a means for creating sequence diversity. Their marked overrepresentation in genomes, and largely unchanging density from the lowest to the highest organisms, indicate their selection over the course of evolution. The mutagenicity at such sites in many human genes is associated with loss of function of key proteins responsible for diverse diseases.
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Affiliation(s)
- Jacques R Fresco
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544; ,
| | - Olga Amosova
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544; ,
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28
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Bioinformatic analysis of riboswitch structures uncovers variant classes with altered ligand specificity. Proc Natl Acad Sci U S A 2017; 114:E2077-E2085. [PMID: 28265071 DOI: 10.1073/pnas.1619581114] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Riboswitches are RNAs that form complex, folded structures that selectively bind small molecules or ions. As with certain groups of protein enzymes and receptors, some riboswitch classes have evolved to change their ligand specificity. We developed a procedure to systematically analyze known riboswitch classes to find additional variants that have altered their ligand specificity. This approach uses multiple-sequence alignments, atomic-resolution structural information, and riboswitch gene associations. Among the discoveries are unique variants of the guanine riboswitch class that most tightly bind the nucleoside 2'-deoxyguanosine. In addition, we identified variants of the glycine riboswitch class that no longer recognize this amino acid, additional members of a rare flavin mononucleotide (FMN) variant class, and also variants of c-di-GMP-I and -II riboswitches that might recognize different bacterial signaling molecules. These findings further reveal the diverse molecular sensing capabilities of RNA, which highlights the potential for discovering a large number of additional natural riboswitch classes.
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29
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Nuthanakanti A, Boerneke MA, Hermann T, Srivatsan SG. Structure of the Ribosomal RNA Decoding Site Containing a Selenium-Modified Responsive Fluorescent Ribonucleoside Probe. Angew Chem Int Ed Engl 2017; 56:2640-2644. [PMID: 28156044 PMCID: PMC5397316 DOI: 10.1002/anie.201611700] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/17/2017] [Indexed: 12/22/2022]
Abstract
Comprehensive understanding of the structure–function relationship of RNA both in real time and at atomic level will have a profound impact in advancing our understanding of RNA functions in biology. Here, we describe the first example of a multifunctional nucleoside probe, containing a conformation‐sensitive fluorophore and an anomalous X‐ray diffraction label (5‐selenophene uracil), which enables the correlation of RNA conformation and recognition under equilibrium and in 3D. The probe incorporated into the bacterial ribosomal RNA decoding site, fluorescently reports antibiotic binding and provides diffraction information in determining the structure without distorting native RNA fold. Further, by comparing solution binding data and crystal structure, we gained insight on how the probe senses ligand‐induced conformational change in RNA. Taken together, our nucleoside probe represents a new class of biophysical tool that would complement available tools for functional RNA investigations.
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Affiliation(s)
- Ashok Nuthanakanti
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India
| | - Mark A Boerneke
- Department of Chemistry and Biochemistry, Center for Drug Discovery Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Thomas Hermann
- Department of Chemistry and Biochemistry, Center for Drug Discovery Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India
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30
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Nuthanakanti A, Boerneke MA, Hermann T, Srivatsan SG. Structure of the Ribosomal RNA Decoding Site Containing a Selenium-Modified Responsive Fluorescent Ribonucleoside Probe. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611700] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Ashok Nuthanakanti
- Department of Chemistry; Indian Institute of Science Education and Research; Dr. Homi Bhabha Road, Pashan Pune 411008 India
| | - Mark A. Boerneke
- Department of Chemistry and Biochemistry; Center for Drug Discovery Innovation; University of California, San Diego; 9500 Gilman Drive La Jolla CA 92093 USA
| | - Thomas Hermann
- Department of Chemistry and Biochemistry; Center for Drug Discovery Innovation; University of California, San Diego; 9500 Gilman Drive La Jolla CA 92093 USA
| | - Seergazhi G. Srivatsan
- Department of Chemistry; Indian Institute of Science Education and Research; Dr. Homi Bhabha Road, Pashan Pune 411008 India
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31
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Chandra V, Hannan Z, Xu H, Mandal M. Single-molecule analysis reveals multi-state folding of a guanine riboswitch. Nat Chem Biol 2016; 13:194-201. [PMID: 27941758 DOI: 10.1038/nchembio.2252] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 10/03/2016] [Indexed: 12/29/2022]
Abstract
Guanine-responsive riboswitches undergo ligand-dependent structural rearrangements to control gene expression by transcription termination. While the molecular basis for ligand recognition is well established, the associated structural rearrangements and the kinetics involved in the formation of the aptamer domain are less well understood. Using high-resolution optical tweezers, we followed the folding trajectories of a single molecule of the xpt-pbuX guanine aptamer from Bacillus subtilis. We report a rapid six-state conformational rearrangement, in which three of the states are guanine dependent, during the transition from the linear to the native receptor conformation. The folding completes in <1 s. The force-dependent equilibrium kinetics and the mutational data indicated that the flexible J2-J3 junction undergoes a ligand-dependent conformational switching, which triggers the formation of the long-range tertiary interactions and the P1 helix. In the absence of the right ligand, the junction failed to initiate the series of conformational rearrangements required for the riboswitch activities.
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Affiliation(s)
- Vishnu Chandra
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Zain Hannan
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Huizhong Xu
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Maumita Mandal
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.,Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.,Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
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32
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Challier L, Miranda-Castro R, Barbe B, Fave C, Limoges B, Peyrin E, Ravelet C, Fiore E, Labbé P, Coche-Guérente L, Ennifar E, Bec G, Dumas P, Mavré F, Noël V. Multianalytical Study of the Binding between a Small Chiral Molecule and a DNA Aptamer: Evidence for Asymmetric Steric Effect upon 3'- versus 5'-End Sequence Modification. Anal Chem 2016; 88:11963-11971. [PMID: 27934108 DOI: 10.1021/acs.analchem.6b04046] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Nucleic acid aptamers are involved in a broad field of applications ranging from therapeutics to analytics. Deciphering the binding mechanisms between aptamers and small ligands is therefore crucial to improve and optimize existing applications and to develop new ones. Particularly interesting is the enantiospecific binding mechanism involving small molecules with nonprestructured aptamers. One archetypal example is the chiral binding between l-tyrosinamide and its 49-mer aptamer for which neither structural nor mechanistic information is available. In the present work, we have taken advantage of a multiple analytical characterization strategy (i.e., using electroanalytical techniques such as kinetic rotating droplet electrochemistry, fluorescence polarization, isothermal titration calorimetry, and quartz crystal microbalance) for interpreting the nature of binding process. Screening of the binding thermodynamics and kinetics with a wide range of aptamer sequences revealed the lack of symmetry between the two ends of the 23-mer minimal binding sequence, showing an unprecedented influence of the 5' aptamer modification on the bimolecular binding rate constant kon and no significant effect on the dissociation rate constant koff. The results we have obtained lead us to conclude that the enantiospecific binding reaction occurs through an induced-fit mechanism, wherein the ligand promotes a primary nucleation binding step near the 5'-end of the aptamer followed by a directional folding of the aptamer around its target from 5'-end to 3'-end. Functionalization of the 5'-end position by a chemical label, a polydA tail, a protein, or a surface influences the kinetic/thermodynamic constants up to 2 orders of magnitude in the extreme case of a surface immobilized aptamer, while significantly weaker effect is observed for a 3'-end modification. The reason is that steric hindrance must be overcome to nucleate the binding complex in the presence of a modification near the nucleation site.
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Affiliation(s)
- Lylian Challier
- ITODYS, UMR 7086 CNRS, Université Paris Diderot, Sorbonne Paris Cité , 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
| | - Rebeca Miranda-Castro
- ITODYS, UMR 7086 CNRS, Université Paris Diderot, Sorbonne Paris Cité , 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
| | - Bertrand Barbe
- ITODYS, UMR 7086 CNRS, Université Paris Diderot, Sorbonne Paris Cité , 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
| | - Claire Fave
- Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité , 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
| | - Benoît Limoges
- Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité , 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
| | - Eric Peyrin
- Département de Pharmacochimie Moléculaire, UMR 5063 CNRS, Université Grenoble Alpes , 470 rue de la chimie, 38400 Saint-Martin d'Hères, France
| | - Corinne Ravelet
- Département de Pharmacochimie Moléculaire, UMR 5063 CNRS, Université Grenoble Alpes , 470 rue de la chimie, 38400 Saint-Martin d'Hères, France
| | - Emmanuelle Fiore
- Département de Pharmacochimie Moléculaire, UMR 5063 CNRS, Université Grenoble Alpes , 470 rue de la chimie, 38400 Saint-Martin d'Hères, France
| | - Pierre Labbé
- Département de Chimie Moléculaire, CNRS, UMR 5250, Université Grenoble Alpes , FR 2607, 570 rue de la chimie, B.P. 53, 38400 Grenoble, France
| | - Liliane Coche-Guérente
- Département de Chimie Moléculaire, CNRS, UMR 5250, Université Grenoble Alpes , FR 2607, 570 rue de la chimie, B.P. 53, 38400 Grenoble, France
| | - Eric Ennifar
- "Architecture et Réactivité de l'ARN", Biophysique et Biologie Structurale, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg , 15 rue René Descartes, 67084 Strasbourg, France
| | - Guillaume Bec
- "Architecture et Réactivité de l'ARN", Biophysique et Biologie Structurale, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg , 15 rue René Descartes, 67084 Strasbourg, France
| | - Philippe Dumas
- "Architecture et Réactivité de l'ARN", Biophysique et Biologie Structurale, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg , 15 rue René Descartes, 67084 Strasbourg, France
| | - François Mavré
- Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité , 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
| | - Vincent Noël
- ITODYS, UMR 7086 CNRS, Université Paris Diderot, Sorbonne Paris Cité , 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
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33
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Sutton JL, Pollack L. Tuning RNA Flexibility with Helix Length and Junction Sequence. Biophys J 2016; 109:2644-2653. [PMID: 26682821 DOI: 10.1016/j.bpj.2015.10.039] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 10/25/2015] [Accepted: 10/27/2015] [Indexed: 12/11/2022] Open
Abstract
The increasing awareness of RNA's central role in biology calls for a new understanding of how RNAs, like proteins, recognize biological partners. Because RNA is inherently flexible, it assumes a variety of conformations. This conformational flexibility can be a critical aspect of how RNA attracts and binds molecular partners. Structurally, RNA consists of rigid basepaired duplexes, separated by flexible non-basepaired regions. Here, using an RNA system consisting of two short helices, connected by a single-stranded (non-basepaired) junction, we explore the role of helix length and junction sequence in determining the range of conformations available to a model RNA. Single-molecule Förster resonance energy transfer reports on the RNA conformation as a function of either mono- or divalent ion concentration. Electrostatic repulsion between helices dominates at low salt concentration, whereas junction sequence effects determine the conformations at high salt concentration. Near physiological salt concentrations, RNA conformation is sensitive to both helix length and junction sequence, suggesting a means for sensitively tuning RNA conformations.
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Affiliation(s)
- Julie L Sutton
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York.
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34
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Perez-Gonzalez C, Lafontaine DA, Penedo JC. Fluorescence-Based Strategies to Investigate the Structure and Dynamics of Aptamer-Ligand Complexes. Front Chem 2016; 4:33. [PMID: 27536656 PMCID: PMC4971091 DOI: 10.3389/fchem.2016.00033] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 07/11/2016] [Indexed: 12/11/2022] Open
Abstract
In addition to the helical nature of double-stranded DNA and RNA, single-stranded oligonucleotides can arrange themselves into tridimensional structures containing loops, bulges, internal hairpins and many other motifs. This ability has been used for more than two decades to generate oligonucleotide sequences, so-called aptamers, that can recognize certain metabolites with high affinity and specificity. More recently, this library of artificially-generated nucleic acid aptamers has been expanded by the discovery that naturally occurring RNA sequences control bacterial gene expression in response to cellular concentration of a given metabolite. The application of fluorescence methods has been pivotal to characterize in detail the structure and dynamics of these aptamer-ligand complexes in solution. This is mostly due to the intrinsic high sensitivity of fluorescence methods and also to significant improvements in solid-phase synthesis, post-synthetic labeling strategies and optical instrumentation that took place during the last decade. In this work, we provide an overview of the most widely employed fluorescence methods to investigate aptamer structure and function by describing the use of aptamers labeled with a single dye in fluorescence quenching and anisotropy assays. The use of 2-aminopurine as a fluorescent analog of adenine to monitor local changes in structure and fluorescence resonance energy transfer (FRET) to follow long-range conformational changes is also covered in detail. The last part of the review is dedicated to the application of fluorescence techniques based on single-molecule microscopy, a technique that has revolutionized our understanding of nucleic acid structure and dynamics. We finally describe the advantages of monitoring ligand-binding and conformational changes, one molecule at a time, to decipher the complexity of regulatory aptamers and summarize the emerging folding and ligand-binding models arising from the application of these single-molecule FRET microscopy techniques.
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Affiliation(s)
- Cibran Perez-Gonzalez
- Laboratory for Biophysics and Biomolecular Dynamics, SUPA School of Physics and Astronomy, University of St. AndrewsSt Andrews, UK
| | - Daniel A. Lafontaine
- RNA Group, Department of Biology, Faculty of Science, Université de SherbrookeSherbrooke, QC, Canada
| | - J. Carlos Penedo
- Laboratory for Biophysics and Biomolecular Dynamics, SUPA School of Physics and Astronomy, University of St. AndrewsSt Andrews, UK
- Laboratory for Biophysics and Biomolecular Dynamics, Biomedical Sciences Research Complex, School of Biology, University of St. AndrewsSt. Andrews, UK
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35
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Esquiaqui JM, Sherman EM, Ye JD, Fanucci GE. Conformational Flexibility and Dynamics of the Internal Loop and Helical Regions of the Kink–Turn Motif in the Glycine Riboswitch by Site-Directed Spin-Labeling. Biochemistry 2016; 55:4295-305. [DOI: 10.1021/acs.biochem.6b00287] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jackie M. Esquiaqui
- Department
of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
| | - Eileen M. Sherman
- Department
of Chemistry, University of Central Florida, 4000 Central Florida Boulevard, Orlando, Florida 32816, United States
| | - Jing-Dong Ye
- Department
of Chemistry, University of Central Florida, 4000 Central Florida Boulevard, Orlando, Florida 32816, United States
| | - Gail E. Fanucci
- Department
of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
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36
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Coarse-grained modeling of RNA 3D structure. Methods 2016; 103:138-56. [PMID: 27125734 DOI: 10.1016/j.ymeth.2016.04.026] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Revised: 04/21/2016] [Accepted: 04/22/2016] [Indexed: 12/21/2022] Open
Abstract
Functional RNA molecules depend on three-dimensional (3D) structures to carry out their tasks within the cell. Understanding how these molecules interact to carry out their biological roles requires a detailed knowledge of RNA 3D structure and dynamics as well as thermodynamics, which strongly governs the folding of RNA and RNA-RNA interactions as well as a host of other interactions within the cellular environment. Experimental determination of these properties is difficult, and various computational methods have been developed to model the folding of RNA 3D structures and their interactions with other molecules. However, computational methods also have their limitations, especially when the biological effects demand computation of the dynamics beyond a few hundred nanoseconds. For the researcher confronted with such challenges, a more amenable approach is to resort to coarse-grained modeling to reduce the number of data points and computational demand to a more tractable size, while sacrificing as little critical information as possible. This review presents an introduction to the topic of coarse-grained modeling of RNA 3D structures and dynamics, covering both high- and low-resolution strategies. We discuss how physics-based approaches compare with knowledge based methods that rely on databases of information. In the course of this review, we discuss important aspects in the reasoning process behind building different models and the goals and pitfalls that can result.
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37
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Weinreb C, Riesselman AJ, Ingraham JB, Gross T, Sander C, Marks DS. 3D RNA and Functional Interactions from Evolutionary Couplings. Cell 2016; 165:963-75. [PMID: 27087444 DOI: 10.1016/j.cell.2016.03.030] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 01/15/2016] [Accepted: 03/18/2016] [Indexed: 11/18/2022]
Abstract
Non-coding RNAs are ubiquitous, but the discovery of new RNA gene sequences far outpaces the research on the structure and functional interactions of these RNA gene sequences. We mine the evolutionary sequence record to derive precise information about the function and structure of RNAs and RNA-protein complexes. As in protein structure prediction, we use maximum entropy global probability models of sequence co-variation to infer evolutionarily constrained nucleotide-nucleotide interactions within RNA molecules and nucleotide-amino acid interactions in RNA-protein complexes. The predicted contacts allow all-atom blinded 3D structure prediction at good accuracy for several known RNA structures and RNA-protein complexes. For unknown structures, we predict contacts in 160 non-coding RNA families. Beyond 3D structure prediction, evolutionary couplings help identify important functional interactions-e.g., at switch points in riboswitches and at a complex nucleation site in HIV. Aided by increasing sequence accumulation, evolutionary coupling analysis can accelerate the discovery of functional interactions and 3D structures involving RNA.
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Affiliation(s)
- Caleb Weinreb
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Adam J Riesselman
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Program in Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - John B Ingraham
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Torsten Gross
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Institute of Pathology, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Chris Sander
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Debora S Marks
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
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38
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Frener M, Micura R. Conformational Rearrangements of Individual Nucleotides during RNA-Ligand Binding Are Rate-Differentiated. J Am Chem Soc 2016; 138:3627-30. [PMID: 26974261 PMCID: PMC4959565 DOI: 10.1021/jacs.5b11876] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A pronounced rate differentiation has been found for conformational rearrangements of individual nucleobases that occur during ligand recognition of the preQ1 class-I riboswitch aptamer from Thermoanaerobacter tengcongensis. Rate measurements rely on the 2ApFold approach by analyzing the fluorescence response of riboswitch variants, each with a single, strategically positioned 2-aminopurine nucleobase substitution. Observed rate discrimination between the fastest and the slowest conformational adaption is 22-fold, with the largest rate observed for the rearrangement of a nucleoside directly at the binding site and the smallest rate observed for the 3'-unpaired nucleoside that stacks onto the pseudo-knot-closing Watson-Crick base pair. Our findings provide novel insights into how compact, prefolded RNAs that follow the induced-fit recognition mechanism adapt local structural elements in response to ligand binding on a rather broad time scale and how this process culminates in a structural signal that is responsible for efficient downregulation of ribosomal translation.
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Affiliation(s)
- Marina Frener
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, 6020 Innsbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, 6020 Innsbruck, Austria
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39
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Guedich S, Puffer-Enders B, Baltzinger M, Hoffmann G, Da Veiga C, Jossinet F, Thore S, Bec G, Ennifar E, Burnouf D, Dumas P. Quantitative and predictive model of kinetic regulation by E. coli TPP riboswitches. RNA Biol 2016; 13:373-90. [PMID: 26932506 PMCID: PMC4841613 DOI: 10.1080/15476286.2016.1142040] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Riboswitches are non-coding elements upstream or downstream of mRNAs that, upon binding of a specific ligand, regulate transcription and/or translation initiation in bacteria, or alternative splicing in plants and fungi. We have studied thiamine pyrophosphate (TPP) riboswitches regulating translation of thiM operon and transcription and translation of thiC operon in E. coli, and that of THIC in the plant A. thaliana. For all, we ascertained an induced-fit mechanism involving initial binding of the TPP followed by a conformational change leading to a higher-affinity complex. The experimental values obtained for all kinetic and thermodynamic parameters of TPP binding imply that the regulation by A. thaliana riboswitch is governed by mass-action law, whereas it is of kinetic nature for the two bacterial riboswitches. Kinetic regulation requires that the RNA polymerase pauses after synthesis of each riboswitch aptamer to leave time for TPP binding, but only when its concentration is sufficient. A quantitative model of regulation highlighted how the pausing time has to be linked to the kinetic rates of initial TPP binding to obtain an ON/OFF switch in the correct concentration range of TPP. We verified the existence of these pauses and the model prediction on their duration. Our analysis also led to quantitative estimates of the respective efficiency of kinetic and thermodynamic regulations, which shows that kinetically regulated riboswitches react more sharply to concentration variation of their ligand than thermodynamically regulated riboswitches. This rationalizes the interest of kinetic regulation and confirms empirical observations that were obtained by numerical simulations.
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Affiliation(s)
- Sondés Guedich
- a IBMC-CNRS, Biophysique et Biologie Structurale, Architecture et Réactivité de l'ARN, Université de Strasbourg , Strasbourg , France
| | - Barbara Puffer-Enders
- a IBMC-CNRS, Biophysique et Biologie Structurale, Architecture et Réactivité de l'ARN, Université de Strasbourg , Strasbourg , France
| | - Mireille Baltzinger
- b IBMC-CNRS, Régulations post-transcriptionnelles et nutrition, Architecture et Réactivité de l'ARN, Université de Strasbourg , Strasbourg , France
| | | | - Cyrielle Da Veiga
- a IBMC-CNRS, Biophysique et Biologie Structurale, Architecture et Réactivité de l'ARN, Université de Strasbourg , Strasbourg , France
| | - Fabrice Jossinet
- d IBMC-CNRS, Evolution des ARN non codants chez la levure, Architecture et Réactivité de l'ARN, Université de Strasbourg , Strasbourg , France
| | - Stéphane Thore
- e Université de Bordeaux, Institut Européen de Chimie et Biologie, ARNA laboratory; INSERM-U1212; CNRS-UMR5320 ; Bordeaux , France
| | - Guillaume Bec
- a IBMC-CNRS, Biophysique et Biologie Structurale, Architecture et Réactivité de l'ARN, Université de Strasbourg , Strasbourg , France
| | - Eric Ennifar
- a IBMC-CNRS, Biophysique et Biologie Structurale, Architecture et Réactivité de l'ARN, Université de Strasbourg , Strasbourg , France
| | - Dominique Burnouf
- a IBMC-CNRS, Biophysique et Biologie Structurale, Architecture et Réactivité de l'ARN, Université de Strasbourg , Strasbourg , France
| | - Philippe Dumas
- a IBMC-CNRS, Biophysique et Biologie Structurale, Architecture et Réactivité de l'ARN, Université de Strasbourg , Strasbourg , France
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40
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Boniecki MJ, Lach G, Dawson WK, Tomala K, Lukasz P, Soltysinski T, Rother KM, Bujnicki JM. SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction. Nucleic Acids Res 2015; 44:e63. [PMID: 26687716 PMCID: PMC4838351 DOI: 10.1093/nar/gkv1479] [Citation(s) in RCA: 232] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 12/05/2015] [Indexed: 01/08/2023] Open
Abstract
RNA molecules play fundamental roles in cellular processes. Their function and interactions with other biomolecules are dependent on the ability to form complex three-dimensional (3D) structures. However, experimental determination of RNA 3D structures is laborious and challenging, and therefore, the majority of known RNAs remain structurally uncharacterized. Here, we present SimRNA: a new method for computational RNA 3D structure prediction, which uses a coarse-grained representation, relies on the Monte Carlo method for sampling the conformational space, and employs a statistical potential to approximate the energy and identify conformations that correspond to biologically relevant structures. SimRNA can fold RNA molecules using only sequence information, and, on established test sequences, it recapitulates secondary structure with high accuracy, including correct prediction of pseudoknots. For modeling of complex 3D structures, it can use additional restraints, derived from experimental or computational analyses, including information about secondary structure and/or long-range contacts. SimRNA also can be used to analyze conformational landscapes and identify potential alternative structures.
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Affiliation(s)
- Michal J Boniecki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Grzegorz Lach
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Wayne K Dawson
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Konrad Tomala
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Pawel Lukasz
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Tomasz Soltysinski
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Kristian M Rother
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
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41
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Heddi B, Martín-Pintado N, Serimbetov Z, Kari TMA, Phan AT. G-quadruplexes with (4n - 1) guanines in the G-tetrad core: formation of a G-triad·water complex and implication for small-molecule binding. Nucleic Acids Res 2015; 44:910-6. [PMID: 26673723 PMCID: PMC4737152 DOI: 10.1093/nar/gkv1357] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 11/21/2015] [Indexed: 01/13/2023] Open
Abstract
G-quadruplexes are non-canonical structures of nucleic acids, in which guanine bases form planar G-tetrads (G·G·G·G) that stack on each other in the core of the structure. G-quadruplexes generally contain multiple times of four (4n) guanines in the core. Here, we study the structure of G-quadruplexes with only (4n - 1) guanines in the core. The solution structure of a DNA sequence containing 11 guanines showed the formation of a parallel G-quadruplex involving two G-tetrads and one G-triad with a vacant site. Molecular dynamics simulation established the formation of a stable G-triad·water complex, where water molecules mimic the position of the missing guanine in the vacant site. The concept of forming G-quadruplexes with missing guanines in the core broadens the current definition of G-quadruplex-forming sequences. The potential ability of such structures to bind different metabolites, including guanine, guanosine and GTP, in the vacant site, could have biological implications in regulatory functions. Formation of this unique binding pocket in the G-triad could be used as a specific target in drug design.
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Affiliation(s)
- Brahim Heddi
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
| | - Nerea Martín-Pintado
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
| | - Zhalgas Serimbetov
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
| | | | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
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42
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Jones CP, Ferré-D'Amaré AR. Recognition of the bacterial alarmone ZMP through long-distance association of two RNA subdomains. Nat Struct Mol Biol 2015; 22:679-85. [PMID: 26280533 PMCID: PMC4824399 DOI: 10.1038/nsmb.3073] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 07/22/2015] [Indexed: 12/22/2022]
Abstract
The bacterial alarmone 5-aminoimidazole-4-carboxamide riboside 5'-triphosphate (ZTP), derived from the monophosphorylated purine precursor ZMP, accumulates during folate starvation. ZTP regulates genes involved in purine and folate metabolism through a cognate riboswitch. The linker connecting this riboswitch’s two sub-domains varies in length by over 100 nucleotides. We report the co-crystal structure of the Fusobacterium ulcerans riboswitch bound to ZMP, which spans the two sub-domains whose interface also comprises a pseudoknot and ribose zipper. The riboswitch recognizes the carboxamide oxygen of ZMP through an unprecedented inner-sphere coordination with a Mg2+ ion. We demonstrate that the affinity of the riboswitch for ZMP is modulated by the linker length. Notably, ZMP can bind to the two sub-domains together even when synthesized as separate RNAs. The ZTP riboswitch demonstrates how specific small-molecule binding can drive association of distant non-coding RNA domains to regulate gene expression.
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Affiliation(s)
- Christopher P Jones
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Adrian R Ferré-D'Amaré
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
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43
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Gong S, Wang Y, Zhang W. The regulation mechanism ofyitJandmetFriboswitches. J Chem Phys 2015; 143:045103. [DOI: 10.1063/1.4927390] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Affiliation(s)
- Sha Gong
- Department of Physics, Wuhan University, Wuhan, Hubei 430072, People’s Republic of China
| | - Yujie Wang
- Department of Physics, Wuhan University, Wuhan, Hubei 430072, People’s Republic of China
| | - Wenbing Zhang
- Department of Physics, Wuhan University, Wuhan, Hubei 430072, People’s Republic of China
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44
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Vakulskas CA, Potts AH, Babitzke P, Ahmer BMM, Romeo T. Regulation of bacterial virulence by Csr (Rsm) systems. Microbiol Mol Biol Rev 2015; 79:193-224. [PMID: 25833324 PMCID: PMC4394879 DOI: 10.1128/mmbr.00052-14] [Citation(s) in RCA: 243] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Most bacterial pathogens have the remarkable ability to flourish in the external environment and in specialized host niches. This ability requires their metabolism, physiology, and virulence factors to be responsive to changes in their surroundings. It is no surprise that the underlying genetic circuitry that supports this adaptability is multilayered and exceedingly complex. Studies over the past 2 decades have established that the CsrA/RsmA proteins, global regulators of posttranscriptional gene expression, play important roles in the expression of virulence factors of numerous proteobacterial pathogens. To accomplish these tasks, CsrA binds to the 5' untranslated and/or early coding regions of mRNAs and alters translation, mRNA turnover, and/or transcript elongation. CsrA activity is regulated by noncoding small RNAs (sRNAs) that contain multiple CsrA binding sites, which permit them to sequester multiple CsrA homodimers away from mRNA targets. Environmental cues sensed by two-component signal transduction systems and other regulatory factors govern the expression of the CsrA-binding sRNAs and, ultimately, the effects of CsrA on secretion systems, surface molecules and biofilm formation, quorum sensing, motility, pigmentation, siderophore production, and phagocytic avoidance. This review presents the workings of the Csr system, the paradigm shift that it generated for understanding posttranscriptional regulation, and its roles in virulence networks of animal and plant pathogens.
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Affiliation(s)
- Christopher A Vakulskas
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | - Anastasia H Potts
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | - Paul Babitzke
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Brian M M Ahmer
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Tony Romeo
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
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45
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Campbell ZT, Wickens M. Probing RNA-protein networks: biochemistry meets genomics. Trends Biochem Sci 2015; 40:157-64. [PMID: 25636997 DOI: 10.1016/j.tibs.2015.01.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 01/05/2015] [Accepted: 01/06/2015] [Indexed: 12/26/2022]
Abstract
RNA-protein interactions are pervasive. The specificity of these interactions dictates which RNAs are controlled by what protein. Here we describe a class of revolutionary new methods that enable global views of RNA-binding specificity in vitro, for both single proteins and multiprotein complexes. These methods provide insight into central issues in RNA regulation in living cells, including understanding the balance between free and bound components, the basis for exclusion of binding sites, detection of binding events in the absence of discernible regulatory elements, and new approaches to targeting endogenous transcripts by design. Comparisons of in vitro and in vivo binding provide a foundation for comprehensive understanding of the biochemistry of protein-mediated RNA regulatory networks.
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Affiliation(s)
- Zachary T Campbell
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA
| | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA.
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46
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Gong S, Wang Y, Zhang W. Kinetic regulation mechanism of pbuE riboswitch. J Chem Phys 2015; 142:015103. [DOI: 10.1063/1.4905214] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Sha Gong
- Department of Physics, Wuhan University, Wuhan, Hubei 430072, People’s Republic of China
| | - Yujie Wang
- Department of Physics, Wuhan University, Wuhan, Hubei 430072, People’s Republic of China
| | - Wenbing Zhang
- Department of Physics, Wuhan University, Wuhan, Hubei 430072, People’s Republic of China
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47
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Yu CH, Olsthoorn RC. Monitoring Ribosomal Frameshifting as a Platform to Screen Anti-Riboswitch Drug Candidates. Methods Enzymol 2015; 550:385-93. [DOI: 10.1016/bs.mie.2014.10.041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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48
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Pawar MG, Nuthanakanti A, Srivatsan SG. Heavy atom containing fluorescent ribonucleoside analog probe for the fluorescence detection of RNA-ligand binding. Bioconjug Chem 2014; 24:1367-77. [PMID: 23841942 DOI: 10.1021/bc400194g] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Although numerous biophysical tools have provided effective systems to study nucleic acids, our current knowledge on how RNA structure complements its function is limited. Therefore, development of robust tools to study the structure–function relationship of RNA is highly desired. Toward this endeavor, we have developed a new ribonucleoside analog, based on a (selenophen-2-yl)pyrimidine core, which could serve as a fluorescence probe to study the function of RNA in real time and as an anomalous scattering label (selenium atom) for the phase determination in X-ray crystallography. The fluorescent selenophene-modified uridine analog is minimally perturbing and exhibits probe-like properties such as sensitivity to microenvironment and conformation changes. Utilizing these properties and amicability of the corresponding ribonucleotide analog to enzymatic incorporation, we have synthesized a fluorescent bacterial ribosomal decoding site (A-site) RNA construct and have developed a fluorescence binding assay to effectively monitor the binding of aminoglycoside antibiotics to the A-site. Our results demonstrate that this simple approach of building a dual probe could provide new avenues to study the structure–function relationship of not only nucleic acids, but also other biomacromolecules.
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49
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Narayan S, Kombrabail MH, Das S, Singh H, Chary KVR, Rao BJ, Krishnamoorthy G. Site-specific fluorescence dynamics in an RNA 'thermometer' reveals the role of ribosome binding in its temperature-sensitive switch function. Nucleic Acids Res 2014; 43:493-503. [PMID: 25477380 PMCID: PMC4288164 DOI: 10.1093/nar/gku1264] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
RNA thermometers control the translation of several heat shock and virulence genes by their temperature-sensitive structural transitions. Changes in the structure and dynamics of MiniROSE RNA, which regulates translation in the temperature range of 20–45°C, were studied by site specifically replacing seven adenine residues with the fluorescent analog, 2-aminopurine (2-AP), one at a time. Dynamic fluorescence observables of 2-AP-labeled RNAs were compared in their free versus ribosome-bound states for the first time. Noticeably, position dependence of fluorescence observables, which was prominent at 20°C, was persistent even at 45ºC, suggesting the persistence of structural integrity up to 45ºC. Interestingly, position-dependent dispersion of fluorescence lifetime and quenching constant at 45°C was ablated in ribosome-bound state, when compared to those at 20°C, underscoring loss of structural integrity at 45°C, in ribosome-bound RNA. Significant increase in the value of mean lifetime for 2-AP corresponding to Shine–Dalgarno sequences, when the temperature was raised from 20 to 45°C, to values seen in the presence of urea at 45°C was a strong indicator of melting of the 3D structure of MiniROSE RNA at 45°C, only when it was ribosome bound. Taken all together, we propose a model where we invoke that ribosome binding of the RNA thermometer critically regulates temperature sensing functions in MiniROSE RNA.
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Affiliation(s)
- Satya Narayan
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Mamta H Kombrabail
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Sudipta Das
- Tata Institute of Fundamental Research, Center for Interdisciplinary Sciences, Hyderabad 500075, India
| | - Himanshu Singh
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Kandala V R Chary
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Basuthkar J Rao
- Department of Chemistry, Indian Institute of Technology, Kanpur 208016, India
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50
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Musiani F, Rossetti G, Capece L, Gerger TM, Micheletti C, Varani G, Carloni P. Molecular dynamics simulations identify time scale of conformational changes responsible for conformational selection in molecular recognition of HIV-1 transactivation responsive RNA. J Am Chem Soc 2014; 136:15631-7. [PMID: 25313638 PMCID: PMC5521259 DOI: 10.1021/ja507812v] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The HIV-1 Tat protein and several small molecules bind to HIV-1 transactivation responsive RNA (TAR) by selecting sparsely populated but pre-existing conformations. Thus, a complete characterization of TAR conformational ensemble and dynamics is crucial to understand this paradigmatic system and could facilitate the discovery of new antivirals targeting this essential regulatory element. We show here that molecular dynamics simulations can be effectively used toward this goal by bridging the gap between functionally relevant time scales that are inaccessible to current experimental techniques. Specifically, we have performed several independent microsecond long molecular simulations of TAR based on one of the most advanced force fields available for RNA, the parmbsc0 AMBER. Our simulations are first validated against available experimental data, yielding an excellent agreement with measured residual dipolar couplings and order parameter S(2). This contrast with previous molecular dynamics simulations (Salmon et al., J. Am. Chem. Soc. 2013 135, 5457-5466) based on the CHARMM36 force field, which could achieve only modest accord with the experimental RDC values. Next, we direct the computation toward characterizing the internal dynamics of TAR over the microsecond time scale. We show that the conformational fluctuations observed over this previously elusive time scale have a strong functionally oriented character in that they are primed to sustain and assist ligand binding.
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Affiliation(s)
- Francesco Musiani
- Scuola Internazionale Superiore di Studi Avanzati (SISSA/ISAS), via Bonomea 265, 34136 Trieste, Italy
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, 40127 Bologna, Italy
- Institute of Neuroscience and Medicine INM-9 and Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Computational Biophysics, German Research School for Simulation Sciences, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Giulia Rossetti
- Institute of Neuroscience and Medicine INM-9 and Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Computational Biophysics, German Research School for Simulation Sciences, Forschungszentrum Jülich, 52425 Jülich, Germany
- Jülich Supercomputing Centre, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Luciana Capece
- International Centre for Genetic Engineering and Biotechnology, AREA Science Park, Padriciano 99, 34149 Trieste, Italy
| | - Thomas Martin Gerger
- Institute of Neuroscience and Medicine INM-9 and Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Computational Biophysics, German Research School for Simulation Sciences, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Cristian Micheletti
- Scuola Internazionale Superiore di Studi Avanzati (SISSA/ISAS), via Bonomea 265, 34136 Trieste, Italy
| | - Gabriele Varani
- Department of Chemistry and Department of Biochemistry, University of Washington, Seattle, 98195 WA, USA
| | - Paolo Carloni
- Institute of Neuroscience and Medicine INM-9 and Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Computational Biophysics, German Research School for Simulation Sciences, Forschungszentrum Jülich, 52425 Jülich, Germany
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