201
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Strobel EJ, Watters KE, Loughrey D, Lucks JB. RNA systems biology: uniting functional discoveries and structural tools to understand global roles of RNAs. Curr Opin Biotechnol 2016; 39:182-191. [PMID: 27132125 DOI: 10.1016/j.copbio.2016.03.019] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 03/24/2016] [Accepted: 03/31/2016] [Indexed: 12/11/2022]
Abstract
RNAs assume sophisticated structures that are active in myriad cellular processes. In this review, we highlight newly identified ribozymes, riboswitches, and small RNAs, some of which control the function of cellular metabolic and gene expression networks. We then examine recent developments in genome-wide RNA structure probing technologies that are yielding new insights into the structural landscape of the transcriptome. Finally, we discuss how these RNA 'structomic' methods can address emerging questions in RNA systems biology, from the mechanisms behind long non-coding RNAs to new bases for human diseases.
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Affiliation(s)
- Eric J Strobel
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States
| | - Kyle E Watters
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States
| | - David Loughrey
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States
| | - Julius B Lucks
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States.
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202
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Furukawa K, Ramesh A, Zhou Z, Weinberg Z, Vallery T, Winkler WC, Breaker RR. Bacterial riboswitches cooperatively bind Ni(2+) or Co(2+) ions and control expression of heavy metal transporters. Mol Cell 2016; 57:1088-1098. [PMID: 25794617 DOI: 10.1016/j.molcel.2015.02.009] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 11/17/2014] [Accepted: 02/03/2015] [Indexed: 11/19/2022]
Abstract
Bacteria regularly encounter widely varying metal concentrations in their surrounding environment. As metals become depleted or, conversely, accrue to toxicity, microbes will activate cellular responses that act to maintain metal homeostasis. A suite of metal-sensing regulatory ("metalloregulatory") proteins orchestrate these responses by allosterically coupling the selective binding of target metals to the activity of DNA-binding domains. However, we report here the discovery, validation, and structural details of a widespread class of riboswitch RNAs, whose members selectively and tightly bind the low-abundance transition metals, Ni(2+) and Co(2+). These riboswitches bind metal cooperatively, and with affinities in the low micromolar range. The structure of a Co(2+)-bound RNA reveals a network of molecular contacts that explains how it achieves cooperative binding between adjacent sites. These findings reveal that bacteria have evolved to utilize highly selective metalloregulatory riboswitches, in addition to metalloregulatory proteins, for detecting and responding to toxic levels of heavy metals.
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Affiliation(s)
- Kazuhiro Furukawa
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Arati Ramesh
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Zhiyuan Zhou
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Zasha Weinberg
- Howard Hughes Medical Institute, New Haven, CT 06520, USA
| | - Tenaya Vallery
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Wade C Winkler
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA.
| | - Ronald R Breaker
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA; Howard Hughes Medical Institute, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
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203
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Mn(2+)-sensing mechanisms of yybP-ykoY orphan riboswitches. Mol Cell 2016; 57:1110-1123. [PMID: 25794619 DOI: 10.1016/j.molcel.2015.02.016] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 01/30/2015] [Accepted: 02/09/2015] [Indexed: 02/05/2023]
Abstract
Gene regulation in cis by riboswitches is prevalent in bacteria. The yybP-ykoY riboswitch family is quite widespread, yet its ligand and function remained unknown. Here, we characterize the Lactococcus lactis yybP-ykoY orphan riboswitch as a Mn(2+)-dependent transcription-ON riboswitch, with a ∼30-40 μM affinity for Mn(2+). We further determined its crystal structure at 2.7 Å to elucidate the metal sensing mechanism. The riboswitch resembles a hairpin, with two coaxially stacked helices tethered by a four-way junction and a tertiary docking interface. The Mn(2+)-sensing region, strategically located at the highly conserved docking interface, has two metal binding sites. Whereas one site tolerates the binding of either Mg(2+) or Mn(2+), the other site strongly prefers Mn(2+) due to a direct contact from the N7 of an invariable adenosine. Mutagenesis and a Mn(2+)-free E. coli yybP-ykoY structure further reveal that Mn(2+) binding is coupled with stabilization of the Mn(2+)-sensing region and the aptamer domain.
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204
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Dambach M, Sandoval M, Updegrove TB, Anantharaman V, Aravind L, Waters LS, Storz G. The ubiquitous yybP-ykoY riboswitch is a manganese-responsive regulatory element. Mol Cell 2016; 57:1099-1109. [PMID: 25794618 DOI: 10.1016/j.molcel.2015.01.035] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 11/17/2014] [Accepted: 01/23/2015] [Indexed: 11/18/2022]
Abstract
The highly structured, cis-encoded RNA elements known as riboswitches modify gene expression upon binding a wide range of molecules. The yybP-ykoY motif was one of the most broadly distributed and numerous bacterial riboswitches for which the cognate ligand was unknown. Using a combination of in vivo reporter and in vitro expression assays, equilibrium dialysis, and northern analysis, we show that the yybP-ykoY motif responds directly to manganese ions in both Escherichia coli and Bacillus subtilis. The identification of the yybP-ykoY motif as a manganese ion sensor suggests that the genes that are preceded by this motif and encode a diverse set of poorly characterized membrane proteins have roles in metal homeostasis.
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Affiliation(s)
- Michael Dambach
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892-5430, USA
| | - Melissa Sandoval
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892-5430, USA
| | - Taylor B Updegrove
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892-5430, USA
| | - Vivek Anantharaman
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Lauren S Waters
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892-5430, USA
- Department of Chemistry, University of Wisconsin Oshkosh, Oshkosh, WI 54901, USA
| | - Gisela Storz
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892-5430, USA
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205
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Lorenz R, Hofacker IL, Stadler PF. RNA folding with hard and soft constraints. Algorithms Mol Biol 2016; 11:8. [PMID: 27110276 PMCID: PMC4842303 DOI: 10.1186/s13015-016-0070-z] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 04/01/2016] [Indexed: 12/21/2022] Open
Abstract
Background A large class of RNA secondary structure prediction programs uses an elaborate energy model grounded in extensive thermodynamic measurements and exact dynamic programming algorithms. External experimental evidence can be in principle be incorporated by means of hard constraints that restrict the search space or by means of soft constraints that distort the energy model. In particular recent advances in coupling chemical and enzymatic probing with sequencing techniques but also comparative approaches provide an increasing amount of experimental data to be combined with secondary structure prediction. Results Responding to the increasing needs for a versatile and user-friendly inclusion of external evidence into diverse flavors of RNA secondary structure prediction tools we implemented a generic layer of constraint handling into the ViennaRNA Package. It makes explicit use of the conceptual separation of the “folding grammar” defining the search space and the actual energy evaluation, which allows constraints to be interleaved in a natural way between recursion steps and evaluation of the standard energy function. Conclusions The extension of the ViennaRNA Package provides a generic way to include diverse types of constraints into RNA folding algorithms. The computational overhead incurred is negligible in practice. A wide variety of application scenarios can be accommodated by the new framework, including the incorporation of structure probing data, non-standard base pairs and chemical modifications, as well as structure-dependent ligand binding. Electronic supplementary material The online version of this article (doi:10.1186/s13015-016-0070-z) contains supplementary material, which is available to authorized users.
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206
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Litke JL, You M, Jaffrey SR. Developing Fluorogenic Riboswitches for Imaging Metabolite Concentration Dynamics in Bacterial Cells. Methods Enzymol 2016; 572:315-33. [PMID: 27241761 DOI: 10.1016/bs.mie.2016.03.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Genetically encoded small-molecule sensors are important tools for revealing the dynamics of metabolites and other small molecules in live cells over time. We recently developed RNA-based sensors that exhibit fluorescence in proportion to a small-molecule ligand. One class of these RNA-based sensors are termed Spinach riboswitches. These are RNAs that are based on naturally occurring riboswitches, but have been fused to the Spinach aptamer. The resulting RNA is a fluorogenic riboswitch, producing fluorescence upon binding the cognate small-molecule analyte. Here, we describe how to design and optimize these sensors by adjusting critical sequence elements, guided by structural insights from the Spinach aptamer. We provide a stepwise procedure to characterize sensors in vitro and to express sensors in bacteria for live-cell imaging of metabolites. Spinach riboswitch sensors offer a simple method for fluorescence measurement of a wide range of metabolites for which riboswitches exist, including nucleotides and their derivatives, amino acids, cofactors, cations, and anions.
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Affiliation(s)
- J L Litke
- Tri-Institutional Chemical Biology Program at Weill-Cornell Medical College, Rockefeller University, Memorial Sloan-Kettering Cancer Center, New York, NY, United States; Weill Medical College, Cornell University, New York, NY, United States
| | - M You
- Weill Medical College, Cornell University, New York, NY, United States
| | - S R Jaffrey
- Tri-Institutional Chemical Biology Program at Weill-Cornell Medical College, Rockefeller University, Memorial Sloan-Kettering Cancer Center, New York, NY, United States; Weill Medical College, Cornell University, New York, NY, United States.
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207
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Hull CM, Anmangandla A, Bevilacqua PC. Bacterial Riboswitches and Ribozymes Potently Activate the Human Innate Immune Sensor PKR. ACS Chem Biol 2016; 11:1118-27. [PMID: 27011290 DOI: 10.1021/acschembio.6b00081] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The innate immune system provides the first line of defense against pathogens through the recognition of nonspecific patterns in RNA to protect the cell in a generalized way. The human RNA-activated protein kinase, PKR, is a dsRNA binding protein and an essential sensor in the innate immune response, which recognizes viral and bacterial pathogens through their RNAs. Upon activation via RNA-dependent autophosphorylation, PKR phosphorylates the eukaryotic initiation factor eIF2α, leading to termination of translation. PKR has a well-characterized role in recognizing viral RNA, where it binds long stretches of double-stranded RNA nonsequence specifically to promote activation; however, the mechanism by which bacterial RNA activates PKR and the mode by which self RNA avoids activating PKR are unknown. We characterized activation of PKR by three functional bacterial RNAs with pseudoknots and extensive tertiary structure: the cyclic di-GMP riboswitch, the glmS riboswitch-ribozyme, and the twister ribozyme, two of which are ligand-activated. These RNAs were found to activate PKR with comparable potency to long dsRNA. Enzymatic structure mapping in the absence and presence of PKR reveals a clear PKR footprint and provides a structural basis for how these bacterial RNAs activate PKR. In the case of the cyclic di-GMP riboswitch and the glmS riboswitch-ribozyme, PKR appears to dimerize on the peripheral double-stranded regions of the native RNA tertiary structure. Overall, these results provide new insights into how PKR acts as an innate immune signaling protein for the presence of bacteria and suggest a reason for the apparent absence of protein-free riboswitches and ribozymes in the human genome.
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Affiliation(s)
- Chelsea M. Hull
- Department
of Chemistry, Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Ananya Anmangandla
- Department
of Chemistry, Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Philip C. Bevilacqua
- Department
of Chemistry, Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department
of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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208
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Abstract
Riboswitches are RNA elements that control the expression of genes through a variety of mechanisms in response to the specific binding of small-molecule ligands. Since their discovery, riboswitches have shown promise for the artificial control of transcription or translation of target genes, be it for industrial biotechnology, protein expression, metabolic engineering, antimicrobial target validation, or gene function discovery. However, natural riboswitches are often unsuitable for these purposes due to their regulation by small molecules which are already present within the cell. For this reason, research has focused on creating riboswitches that respond to alternative biologically inert ligands or to molecules which are of interest for biosensing. Here we present methods for the development of artificial riboswitches in Gram-negative and Gram-positive bacteria. These methods are based on reengineering natural aptamers to change their ligand specificity toward molecules which do not bind the original aptamer (ie, that are orthogonal to the original). The first approach involves targeted mutagenesis of native riboswitches to change their specificity toward rationally designed synthetic ligand analogs. The second approach involves the fusion of previously validated orthogonal aptamers with native expression platforms to create novel chimeric riboswitches for the microbial target. We establish the applicability of these methods both for the control of exogenous genes as well as for the control of native genes.
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209
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Li S, Hwang XY, Stav S, Breaker RR. The yjdF riboswitch candidate regulates gene expression by binding diverse azaaromatic compounds. RNA (NEW YORK, N.Y.) 2016; 22:530-41. [PMID: 26843526 PMCID: PMC4793209 DOI: 10.1261/rna.054890.115] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 12/10/2015] [Indexed: 05/21/2023]
Abstract
The yjdF motif RNA is an orphan riboswitch candidate that almost exclusively associates with the yjdF protein-coding gene in many bacteria. The function of the YjdF protein is unknown, which has made speculation regarding the natural ligand for this putative riboswitch unusually challenging. By using a structure-probing assay for ligand binding, we found that a surprisingly broad diversity of nitrogen-containing aromatic heterocycles, or "azaaromatics," trigger near-identical changes in the structures adopted by representative yjdF motif RNAs. Regions of the RNA that undergo ligand-induced structural modulation reside primarily in portions of the putative aptamer region that are highly conserved in nucleotide sequence, as is typical for riboswitches. Some azaaromatic molecules are bound by the RNA with nanomolar dissociation constants, and a subset of these ligands activate riboswitch-mediated gene expression in cells. Furthermore, genetic elements most commonly adjacent to the yjdF motif RNA or to the yjdF protein-coding region are homologous to protein regulators implicated in mitigating the toxic effects of diverse phenolic acids or polycyclic compounds. Although the precise type of natural ligand sensed by yjdF motif RNAs remains unknown, our findings suggest that this riboswitch class might serve as part of a genetic response system to toxic or signaling compounds with chemical structures similar to azaaromatics.
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Affiliation(s)
- Sanshu Li
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520-8103, USA
| | - Xue Ying Hwang
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA
| | - Shira Stav
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA
| | - Ronald R Breaker
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520-8103, USA Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8103, USA
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210
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Inuzuka S, Nishimura KI, Kakizawa H, Fujita Y, Furuta H, Matsumura S, Ikawa Y. Mutational analysis of structural elements in a class-I cyclic di-GMP riboswitch to elucidate its regulatory mechanism. J Biochem 2016; 160:153-62. [PMID: 27033943 DOI: 10.1093/jb/mvw026] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 02/21/2016] [Indexed: 12/23/2022] Open
Abstract
The Vc2 riboswitch possesses an aptamer domain belonging to the class-I c-di-GMP riboswitch family. This domain has been analysed and the molecular mechanism by which it recognizes the c-di-GMP ligand has been elucidated. On the other hand, the regulatory mechanism of the full-length Vc2 riboswitch to control its downstream open reading frame (ORF) remains largely unknown. In this study, we performed in vivo reporter assays and in vitro biochemical analyses of the full-length riboswitch and its aptamer domain. We evaluated the results of in vivo and in vitro analyses to elucidate the regulatory mechanism of the Vc2 riboswitch. The present results suggest that recognition of c-di-GMP ligand by the Vc2 riboswitch aptamer domain downregulates expression of its downstream ORF primarily at the translational level.
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Affiliation(s)
- Saki Inuzuka
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Toyama 930-8555, Japan
| | - Kei-Ichiro Nishimura
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Fukuoka 819-0395, Japan
| | - Hitoshi Kakizawa
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Toyama 930-8555, Japan
| | - Yuki Fujita
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Fukuoka 819-0395, Japan
| | - Hiroyuki Furuta
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Fukuoka 819-0395, Japan
| | - Shigeyoshi Matsumura
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Toyama 930-8555, Japan
| | - Yoshiya Ikawa
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Toyama 930-8555, Japan
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211
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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: 19] [Impact Index Per Article: 2.1] [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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212
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Inuzuka S, Matsumura S, Ikawa Y. Optimization of RNA-based c-di-GMP fluorescent sensors through tuning their structural modules. J Biosci Bioeng 2016; 122:183-7. [PMID: 26968125 DOI: 10.1016/j.jbiosc.2016.01.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 01/25/2016] [Accepted: 01/26/2016] [Indexed: 01/31/2023]
Abstract
Cyclic diguanylate (c-di-GMP) is a second messenger of bacteria and its detection is an important issue in basic and applied microbiology. As c-di-GMP riboswitch ligand-binding domains (aptamer domains) capture c-di-GMP with high affinity and selectivity, they are promising platforms for the development of RNA-based c-di-GMP sensors. We analyzed two previously reported c-di-GMP sensor RNAs derived from the Vc2 riboswitch. We also designed and tested their variants, some of which showed improved properties as RNA-based c-di-GMP sensors.
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Affiliation(s)
- Saki Inuzuka
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, 3190 Gofuku, Toyama 930-8555, Japan
| | - Shigeyoshi Matsumura
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, 3190 Gofuku, Toyama 930-8555, Japan
| | - Yoshiya Ikawa
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, 3190 Gofuku, Toyama 930-8555, Japan.
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213
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van der Meulen SB, de Jong A, Kok J. Transcriptome landscape of Lactococcus lactis reveals many novel RNAs including a small regulatory RNA involved in carbon uptake and metabolism. RNA Biol 2016; 13:353-66. [PMID: 26950529 PMCID: PMC4829306 DOI: 10.1080/15476286.2016.1146855] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
RNA sequencing has revolutionized genome-wide transcriptome analyses, and the identification of non-coding regulatory RNAs in bacteria has thus increased concurrently. Here we reveal the transcriptome map of the lactic acid bacterial paradigm Lactococcus lactis MG1363 by employing differential RNA sequencing (dRNA-seq) and a combination of manual and automated transcriptome mining. This resulted in a high-resolution genome annotation of L. lactis and the identification of 60 cis-encoded antisense RNAs (asRNAs), 186 trans-encoded putative regulatory RNAs (sRNAs) and 134 novel small ORFs. Based on the putative targets of asRNAs, a novel classification is proposed. Several transcription factor DNA binding motifs were identified in the promoter sequences of (a)sRNAs, providing insight in the interplay between lactococcal regulatory RNAs and transcription factors. The presence and lengths of 14 putative sRNAs were experimentally confirmed by differential Northern hybridization, including the abundant RNA 6S that is differentially expressed depending on the available carbon source. For another sRNA, LLMGnc_147, functional analysis revealed that it is involved in carbon uptake and metabolism. L. lactis contains 13% leaderless mRNAs (lmRNAs) that, from an analysis of overrepresentation in GO classes, seem predominantly involved in nucleotide metabolism and DNA/RNA binding. Moreover, an A-rich sequence motif immediately following the start codon was uncovered, which could provide novel insight in the translation of lmRNAs. Altogether, this first experimental genome-wide assessment of the transcriptome landscape of L. lactis and subsequent sRNA studies provide an extensive basis for the investigation of regulatory RNAs in L. lactis and related lactococcal species.
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Affiliation(s)
- Sjoerd B van der Meulen
- a Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute , University of Groningen , Groningen , The Netherlands.,b Top Institute Food and Nutrition (TIFN) , Wageningen , The Netherlands
| | - Anne de Jong
- a Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute , University of Groningen , Groningen , The Netherlands.,b Top Institute Food and Nutrition (TIFN) , Wageningen , The Netherlands
| | - Jan Kok
- a Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute , University of Groningen , Groningen , The Netherlands.,b Top Institute Food and Nutrition (TIFN) , Wageningen , The Netherlands
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214
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Zhou H, Zheng C, Su J, Chen B, Fu Y, Xie Y, Tang Q, Chou SH, He J. Characterization of a natural triple-tandem c-di-GMP riboswitch and application of the riboswitch-based dual-fluorescence reporter. Sci Rep 2016; 6:20871. [PMID: 26892868 PMCID: PMC4759541 DOI: 10.1038/srep20871] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 01/11/2016] [Indexed: 12/22/2022] Open
Abstract
c-di-GMP riboswitches are structured RNAs located in the 5'-untranslated regions (5'-UTRs) of mRNAs that regulate expression of downstream genes in response to changing concentrations of the second messenger c-di-GMP. We discovered three complete c-di-GMP riboswitches (Bc3, Bc4 and Bc5 RNA) with similar structures, which are arranged in tandem to constitute a triple-tandem (Bc3-5 RNA) riboswitch in the 5'-UTR of the cspABCDE mRNA in Bacillus thuringiensis subsp. chinensis CT-43. Our results showed that this natural triple-tandem riboswitch controlled the expression of the reporter gene more stringently and digitally than the double-tandem or single riboswitch. A sandwich-like dual-fluorescence reporter was further constructed by fusing the Bc3-5 RNA gene between the two fluorescence protein genes amcyan and turborfp. This reporter strain was found to exhibit detectable fluorescence color changes under bright field in response to intracellular c-di-GMP level altered by induced expression of diguanylate cyclase (DGC) PleD. Using this system, two putative membrane-bound DGCs from B. thuringiensis and Xanthomonas oryzae were verified to be functional by replacing pleD with the corresponding DGC genes. This report represented the first native triple-tandem riboswitch that was applied to serve as a riboswitch-based dual-fluorescence reporter for the efficient and convenient verification of putative DGC activity in vivo.
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Affiliation(s)
- Hang Zhou
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
| | - Cao Zheng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
| | - Jianmei Su
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
| | - Bo Chen
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
| | - Yang Fu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
| | - Yuqun Xie
- Key Laboratory of Fermentation Engineering (Ministry of Education), College of Bioengineering, Hubei University of Technology, Wuhan, Hubei 430068, People's Republic of China
| | - Qing Tang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
| | - Shan-Ho Chou
- Institute of Biochemistry, and NCHU Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Jin He
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
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215
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Linc-ROR induces epithelial-mesenchymal transition and contributes to drug resistance and invasion of breast cancer cells. Tumour Biol 2016; 37:10861-70. [DOI: 10.1007/s13277-016-4909-1] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 01/22/2016] [Indexed: 10/22/2022] Open
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216
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217
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Banerjee C, Singh PK, Shukla P. Microalgal bioengineering for sustainable energy development: Recent transgenesis and metabolic engineering strategies. Biotechnol J 2016; 11:303-14. [DOI: 10.1002/biot.201500284] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 09/15/2015] [Accepted: 01/05/2016] [Indexed: 12/11/2022]
Affiliation(s)
- Chiranjib Banerjee
- Department of Environmental Science & Engineering; Indian School of Mines; Dhanbad Jharkhand India
| | - Puneet Kumar Singh
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology; Maharshi Dayanand University; Rohtak Haryana India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology; Maharshi Dayanand University; Rohtak Haryana India
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218
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Small molecule fluoride toxicity agonists. ACTA ACUST UNITED AC 2016; 22:527-534. [PMID: 25910244 DOI: 10.1016/j.chembiol.2015.03.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 03/09/2015] [Accepted: 03/16/2015] [Indexed: 12/15/2022]
Abstract
Fluoride is a ubiquitous anion that inhibits a wide variety of metabolic processes. Here, we report the identification of a series of compounds that enhance fluoride toxicity in Escherichia coli and Streptococcus mutans. These molecules were isolated by using a high-throughput screen (HTS) for compounds that increase intracellular fluoride levels as determined via a fluoride riboswitch reporter fusion construct. A series of derivatives were synthesized to examine structure-activity relationships, leading to the identification of compounds with improved activity. Thus, we demonstrate that small molecule fluoride toxicity agonists can be identified by HTS from existing chemical libraries by exploiting a natural fluoride riboswitch. In addition, our findings suggest that some molecules might be further optimized to function as binary antibacterial agents when combined with fluoride.
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219
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Duchardt-Ferner E, Gottstein-Schmidtke SR, Weigand JE, Ohlenschläger O, Wurm JP, Hammann C, Suess B, Wöhnert J. Eine OH-Gruppe ändert alles: konformative Dynamik als Grundlage für die Ligandenspezifität des Neomycin-bindenden RNA-Schalters. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201507365] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Elke Duchardt-Ferner
- Institut für Molekulare Biowissenschaften und Zentrum für Biomolekulare Magnetische Resonanz (BMRZ); Goethe-Universität Frankfurt; Max-von-Laue-Straße 9 60438 Frankfurt/M Deutschland
| | - Sina R. Gottstein-Schmidtke
- Institut für Molekulare Biowissenschaften und Zentrum für Biomolekulare Magnetische Resonanz (BMRZ); Goethe-Universität Frankfurt; Max-von-Laue-Straße 9 60438 Frankfurt/M Deutschland
| | - Julia E. Weigand
- Fachbereich Biologie; Technische Universität Darmstadt; Schnittspahnstraße 10 64287 Darmstadt Deutschland
| | - Oliver Ohlenschläger
- Biomolekulare NMR-Spektroskopie; Leibniz-Institut für Altersforschung (Fritz-Lipmann-Institut); Beutenbergstraße 11 07745 Jena Deutschland
| | - Jan-Philip Wurm
- Institut für Molekulare Biowissenschaften und Zentrum für Biomolekulare Magnetische Resonanz (BMRZ); Goethe-Universität Frankfurt; Max-von-Laue-Straße 9 60438 Frankfurt/M Deutschland
| | - Christian Hammann
- Ribogenetics Biochemistry Lab; Jacobs Universität Bremen; 28759 Bremen Deutschland
| | - Beatrix Suess
- Fachbereich Biologie; Technische Universität Darmstadt; Schnittspahnstraße 10 64287 Darmstadt Deutschland
| | - Jens Wöhnert
- Institut für Molekulare Biowissenschaften und Zentrum für Biomolekulare Magnetische Resonanz (BMRZ); Goethe-Universität Frankfurt; Max-von-Laue-Straße 9 60438 Frankfurt/M Deutschland
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220
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Chen B, LeBlanc R, Dayie TK. SAM-II Riboswitch Samples at least Two Conformations in Solution in the Absence of Ligand: Implications for Recognition. Angew Chem Int Ed Engl 2016; 55:2724-7. [PMID: 26800479 DOI: 10.1002/anie.201509997] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 12/18/2015] [Indexed: 11/10/2022]
Abstract
Conformational equilibria are increasingly recognized as pivotal for biological function. Traditional structural analyses provide a static image of conformers in solution that sometimes present conflicting views. From (13) C and (1) H chemical exchange saturation transfer experiments, in concert with ligation and selective labeling strategies, we show that in the absence of metabolite, a Mg(2+) (0-0.5 mm)-bound apo SAM-II riboswitch RNA exists in a minor (≈10 %) partially closed state that rapidly exchanges with a predominantly (≈90 %) open form with a lifetime of ≈32 ms. The base and sugar (H6,C6, H1',C1') chemical shifts of C43 for the dominant conformer are similar to those of a free CMP, but those of the minor apo species are comparable to shifts of CMPs in helical RNA regions. Our results suggest that these transient, low populated states stabilized by Mg(2+) will likely enhance rapid ligand recognition and, we anticipate, will play potentially ubiquitous roles in RNA signaling.
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Affiliation(s)
- Bin Chen
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, Biomolecular Sciences Building (296), 8314 Paint Branch Dr., College Park, MD, 20782, USA
| | - Regan LeBlanc
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, Biomolecular Sciences Building (296), 8314 Paint Branch Dr., College Park, MD, 20782, USA
| | - T Kwaku Dayie
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, Biomolecular Sciences Building (296), 8314 Paint Branch Dr., College Park, MD, 20782, USA.
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221
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Chen B, LeBlanc R, Dayie TK. SAM‐II Riboswitch Samples at least Two Conformations in Solution in the Absence of Ligand: Implications for Recognition. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201509997] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Bin Chen
- Center for Biomolecular Structure and Organization Department of Chemistry and Biochemistry University of Maryland Biomolecular Sciences Building (296), 8314 Paint Branch Dr. College Park MD 20782 USA
| | - Regan LeBlanc
- Center for Biomolecular Structure and Organization Department of Chemistry and Biochemistry University of Maryland Biomolecular Sciences Building (296), 8314 Paint Branch Dr. College Park MD 20782 USA
| | - T. Kwaku Dayie
- Center for Biomolecular Structure and Organization Department of Chemistry and Biochemistry University of Maryland Biomolecular Sciences Building (296), 8314 Paint Branch Dr. College Park MD 20782 USA
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222
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Rinaldi AJ, Lund PE, Blanco MR, Walter NG. The Shine-Dalgarno sequence of riboswitch-regulated single mRNAs shows ligand-dependent accessibility bursts. Nat Commun 2016; 7:8976. [PMID: 26781350 PMCID: PMC4735710 DOI: 10.1038/ncomms9976] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 10/21/2015] [Indexed: 01/20/2023] Open
Abstract
In response to intracellular signals in Gram-negative bacteria, translational riboswitches—commonly embedded in messenger RNAs (mRNAs)—regulate gene expression through inhibition of translation initiation. It is generally thought that this regulation originates from occlusion of the Shine-Dalgarno (SD) sequence upon ligand binding; however, little direct evidence exists. Here we develop Single Molecule Kinetic Analysis of RNA Transient Structure (SiM-KARTS) to investigate the ligand-dependent accessibility of the SD sequence of an mRNA hosting the 7-aminomethyl-7-deazaguanine (preQ1)-sensing riboswitch. Spike train analysis reveals that individual mRNA molecules alternate between two conformational states, distinguished by ‘bursts' of probe binding associated with increased SD sequence accessibility. Addition of preQ1 decreases the lifetime of the SD's high-accessibility (bursting) state and prolongs the time between bursts. In addition, ligand-jump experiments reveal imperfect riboswitching of single mRNA molecules. Such complex ligand sensing by individual mRNA molecules rationalizes the nuanced ligand response observed during bulk mRNA translation. In response to intracellular signals, bacterial translational riboswitches embedded in mRNAs can regulate gene expression through inhibition of translation initiation. Here, the authors describe SiM-KARTS, a novel approach for detecting changes in the structure of single RNA molecules in response to a ligand.
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Affiliation(s)
- Arlie J Rinaldi
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Paul E Lund
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA.,Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Mario R Blanco
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
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223
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The unmasking of 'junk' RNA reveals novel sRNAs: from processed RNA fragments to marooned riboswitches. Curr Opin Microbiol 2016; 30:16-21. [PMID: 26771674 DOI: 10.1016/j.mib.2015.12.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 11/17/2015] [Accepted: 12/09/2015] [Indexed: 11/22/2022]
Abstract
While the notion that RNAs can function as regulators dates back to early molecular studies of gene regulation of the lac operon, it is only over the last decade that the ubiquity and diversity of regulatory RNAs are being realized. Advancements in high throughput sequencing and the adoption of these approaches to rapidly sequence genomes and transcriptomes and to examine gene expression and RNA binding protein specificity have revealed an ever-expanding RNA world. In this review, we focus on recent studies revealing that RNA fragments cleaved from larger coding or noncoding RNAs can have regulatory functions. Additionally, we discuss examples of riboswitches that function in trans as mRNA or protein-binding sRNAs, upending the traditional thinking that these are exclusively cis-acting elements.
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224
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Abstract
All living organisms sense and respond to harmful changes in their intracellular and extracellular environment through complex signaling pathways that lead to changes in gene expression and cellular function in order to maintain homeostasis. Long non-coding RNAs (lncRNAs), a large and heterogeneous group of functional RNAs, play important roles in cellular response to stressful conditions. lncRNAs constitute a significant fraction of the genes differentially expressed in response to diverse stressful stimuli and, once induced, contribute to the regulation of downstream cellular processes, including feedback regulation of key stress response proteins. While many lncRNAs seem to be induced in response to a specific stress, there is significant overlap between lncRNAs induced in response to different stressful stimuli. In addition to stress-induced RNAs, several constitutively expressed lncRNAs also exert a strong regulatory impact on the stress response. Although our understanding of the contribution of lncRNAs to the cellular stress response is still highly rudimentary, the existing data point to the presence of a complex network of lncRNAs, miRNAs, and proteins in regulation of the cellular response to stress.
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Affiliation(s)
- Saba Valadkhan
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
| | - Alberto Valencia-Hipólito
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
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225
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Ohbayashi R, Akai H, Yoshikawa H, Hess WR, Watanabe S. A tightly inducible riboswitch system in Synechocystis sp. PCC 6803. J GEN APPL MICROBIOL 2016; 62:154-9. [DOI: 10.2323/jgam.2016.02.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Ryudo Ohbayashi
- Department of Bioscience, Tokyo University of Agriculture
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST)
| | - Hideto Akai
- Department of Bioscience, Tokyo University of Agriculture
| | - Hirofumi Yoshikawa
- Department of Bioscience, Tokyo University of Agriculture
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST)
| | - Wolfgang R. Hess
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg
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226
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Abstract
Recent studies have revealed that the majority of biological processes are controlled by noncoding RNAs. Among many classes of noncoding RNAs, metabolite-sensing segments of mRNAs called riboswitches are unique. Discovered over a decade ago in all three kingdoms of life, riboswitches specifically and directly interact with various metabolites and regulate expression of multiple genes, often associated with metabolism and transport of small molecules. Thus, riboswitches do not depend on proteins for binding to small molecules and play a role as both metabolite sensors and effectors of gene control. Riboswitches are typically located in the untranslated regions of mRNAs where they form alternative structures in the presence and absence of the ligand and modulate expression of genes through the formation of regulatory elements. To understand the mechanism of the riboswitch-driven gene control, it is important to elucidate how riboswitches interact with cognate and discriminate against non-cognate ligands. Here we outline the methodology to synthesize riboswitch RNAs and prepare riboswitch-ligand complexes for crystallographic and biochemical studies. The chapter describes how to design, prepare, and conduct crystallization screening of riboswitch-ligand complexes. The methodology was refined on crystallographic studies of several riboswitches and can be employed for other types of RNA molecules.
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227
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Zhou LB, Zeng AP. Engineering a Lysine-ON Riboswitch for Metabolic Control of Lysine Production in Corynebacterium glutamicum. ACS Synth Biol 2015; 4:1335-40. [PMID: 26300047 DOI: 10.1021/acssynbio.5b00075] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Riboswitches are natural RNA elements that regulate gene expression by binding a ligand. Here, we demonstrate the possibility of altering a natural lysine-OFF riboswitch from Eschericia coli (ECRS) to a synthetic lysine-ON riboswitch and using it for metabolic control. To this end, a lysine-ON riboswitch library was constructed using tetA-based dual genetic selection. After screening the library, the functionality of the selected lysine-ON riboswitches was examined using a report gene, lacZ. Selected lysine-ON riboswitches were introduced into the lysE gene (encoding a lysine transport protein) of Corynebacterium glutamicum and used to achieve dynamic control of lysine transport in a recombinant lysine-producing strain, C. glutamicum LPECRS, which bears a deregulated aspartokinase and a lysine-OFF riboswitch for dynamic control of the enzyme citrate synthase. Batch fermentation results of the strains showed that the C. glutamicum LPECRS strain with an additional lysine-ON riboswitch for the control of lysE achieved a 21% increase in the yield of lysine compared to that of the C. glutamicum LPECRS strain and even a 89% increase in yield compared to that of the strain with deregulated aspartokinase. This work provides a useful approach to generate lysine-ON riboswitches for C. glutamicum metabolic engineering and demonstrates for the first time a synergetic effect of lysine-ON and -OFF riboswitches for improving lysine production in this industrially important microorganism. The approach can be used to dynamically control other genes and can be applied to other microorganisms.
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Affiliation(s)
- Li-Bang Zhou
- Institute of Bioprocess and
Biosystems Engineering, Hamburg University of Technology, Denickestrasse
15, D-21073 Hamburg, Germany
| | - An-Ping Zeng
- Institute of Bioprocess and
Biosystems Engineering, Hamburg University of Technology, Denickestrasse
15, D-21073 Hamburg, Germany
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228
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Wachsmuth M, Domin G, Lorenz R, Serfling R, Findeiß S, Stadler PF, Mörl M. Design criteria for synthetic riboswitches acting on transcription. RNA Biol 2015; 12:221-31. [PMID: 25826571 DOI: 10.1080/15476286.2015.1017235] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Riboswitches are RNA-based regulators of gene expression composed of a ligand-sensing aptamer domain followed by an overlapping expression platform. The regulation occurs at either the level of transcription (by formation of terminator or antiterminator structures) or translation (by presentation or sequestering of the ribosomal binding site). Due to a modular composition, these elements can be manipulated by combining different aptamers and expression platforms and therefore represent useful tools to regulate gene expression in synthetic biology. Using computationally designed theophylline-dependent riboswitches we show that 2 parameters, terminator hairpin stability and folding traps, have a major impact on the functionality of the designed constructs. These have to be considered very carefully during design phase. Furthermore, a combination of several copies of individual riboswitches leads to a much improved activation ratio between induced and uninduced gene activity and to a linear dose-dependent increase in reporter gene expression. Such serial arrangements of synthetic riboswitches closely resemble their natural counterparts and may form the basis for simple quantitative read out systems for the detection of specific target molecules in the cell.
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Affiliation(s)
- Manja Wachsmuth
- a University of Leipzig ; Institute for Biochemistry ; Leipzig , Germany
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229
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Whisper mutations: cryptic messages within the genetic code. Oncogene 2015; 35:3753-9. [PMID: 26657150 DOI: 10.1038/onc.2015.454] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 10/28/2015] [Accepted: 10/28/2015] [Indexed: 01/17/2023]
Abstract
Recent years have seen a great expansion in our understandings of how silent mutations can drive a disease and that mRNAs are not only mere messengers between the genome and the encoded proteins but also encompass regulatory activities. This review focuses on how silent mutations within open reading frames can affect the functional properties of the encoded protein. We describe how mRNAs exert control of cell biological processes governed by the encoded proteins via translation kinetics, protein folding, mRNA stability, spatio-temporal protein expression and by direct interactions with cellular factors. These examples illustrate how additional levels of information lie within the coding sequences and that the degenerative genetic code is not redundant and have co-evolved with the encoded proteins. Hence, so called synonymous mutations are not always silent but 'whisper'.
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230
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Duchardt-Ferner E, Gottstein-Schmidtke SR, Weigand JE, Ohlenschläger O, Wurm JP, Hammann C, Suess B, Wöhnert J. What a Difference an OH Makes: Conformational Dynamics as the Basis for the Ligand Specificity of the Neomycin-Sensing Riboswitch. Angew Chem Int Ed Engl 2015; 55:1527-30. [PMID: 26661511 DOI: 10.1002/anie.201507365] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Indexed: 01/13/2023]
Abstract
To ensure appropriate metabolic regulation, riboswitches must discriminate efficiently between their target ligands and chemically similar molecules that are also present in the cell. A remarkable example of efficient ligand discrimination is a synthetic neomycin-sensing riboswitch. Paromomycin, which differs from neomycin only by the substitution of a single amino group with a hydroxy group, also binds but does not flip the riboswitch. Interestingly, the solution structures of the two riboswitch-ligand complexes are virtually identical. In this work, we demonstrate that the local loss of key intermolecular interactions at the substitution site is translated through a defined network of intramolecular interactions into global changes in RNA conformational dynamics. The remarkable specificity of this riboswitch is thus based on structural dynamics rather than static structural differences. In this respect, the neomycin riboswitch is a model for many of its natural counterparts.
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Affiliation(s)
- Elke Duchardt-Ferner
- Institut für Molekulare Biowissenschaften and Zentrum für Biomolekulare Magnetische Resonanz (BMRZ), Goethe-Universität Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt/M, Deutschland
| | - Sina R Gottstein-Schmidtke
- Institut für Molekulare Biowissenschaften and Zentrum für Biomolekulare Magnetische Resonanz (BMRZ), Goethe-Universität Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt/M, Deutschland
| | - Julia E Weigand
- Fachbereich Biologie, Technische Universität Darmstadt, Schnittspahnstr. 10, 64287, Darmstadt, Deutschland
| | - Oliver Ohlenschläger
- Biomolekulare NMR-Spektroskopie, Leibniz Institut für Altersforschung (Fritz-Lipmann-Institut), Beutenbergstrasse 11, 07745, Jena, Deutschland
| | - Jan-Philip Wurm
- Institut für Molekulare Biowissenschaften and Zentrum für Biomolekulare Magnetische Resonanz (BMRZ), Goethe-Universität Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt/M, Deutschland
| | - Christian Hammann
- Ribogenetics Biochemistry Lab, Jacobs Universität Bremen, 28759, Bremen, Deutschland
| | - Beatrix Suess
- Fachbereich Biologie, Technische Universität Darmstadt, Schnittspahnstr. 10, 64287, Darmstadt, Deutschland
| | - Jens Wöhnert
- Institut für Molekulare Biowissenschaften and Zentrum für Biomolekulare Magnetische Resonanz (BMRZ), Goethe-Universität Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt/M, Deutschland.
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231
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Identification of RNA Oligonucleotides Binding to Several Proteins from Potential G-Quadruplex Forming Regions in Transcribed Pre-mRNA. Molecules 2015; 20:20832-40. [PMID: 26610452 PMCID: PMC6332122 DOI: 10.3390/molecules201119733] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 11/06/2015] [Accepted: 11/12/2015] [Indexed: 11/16/2022] Open
Abstract
G-quadruplexes (G4s) are noncanonical DNA/RNA structures formed by guanine-rich sequences. Recently, G4s have been found not only in aptamers but also in the genomic DNA and transcribed RNA. In this study, we identified new RNA oligonucleotides working as aptamers by focusing on G4-forming RNAs located within the pre-mRNA. We showed that the G4 in the 5′ UTR and first intron of VEGFA bound to the protein encoded in VEGFA gene, VEGF165, with high affinity. Moreover, G4-forming RNAs located within the PDGFA and the PDGFB introns bound to PDGF-AA and PDGF-BB, respectively, indicating that G4 in the pre-mRNA could be an aptamer. It had been reported that the putative G4-forming RNA sequences are located in some parts of most genes, thus our strategy for aptamer identification could be applicable to other proteins. It has been reported that some G4-forming RNAs in 5′ UTRs are involved in translation control; however, G4-forming excised intronic RNA function has not been revealed previously. Therefore, these findings could not only contribute to the identification of RNA aptamers but also provide new insights into the biological functioning of G4-forming RNAs located within intronic RNA sequences.
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232
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Ren A, Xue Y, Peselis A, Serganov A, Al-Hashimi HM, Patel DJ. Structural and Dynamic Basis for Low-Affinity, High-Selectivity Binding of L-Glutamine by the Glutamine Riboswitch. Cell Rep 2015; 13:1800-13. [PMID: 26655897 DOI: 10.1016/j.celrep.2015.10.062] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 08/17/2015] [Accepted: 10/20/2015] [Indexed: 12/24/2022] Open
Abstract
Naturally occurring L-glutamine riboswitches occur in cyanobacteria and marine metagenomes, where they reside upstream of genes involved in nitrogen metabolism. By combining X-ray, NMR, and MD, we characterized an L-glutamine-dependent conformational transition in the Synechococcus elongatus glutamine riboswitch from tuning fork to L-shaped alignment of stem segments. This transition generates an open ligand-binding pocket with L-glutamine selectivity enforced by Mg(2+)-mediated intermolecular interactions. The transition also stabilizes the P1 helix through a long-range "linchpin" Watson-Crick G-C pair-capping interaction, while melting a short helix below P1 potentially capable of modulating downstream readout. NMR data establish that the ligand-free glutamine riboswitch in Mg(2+) solution exists in a slow equilibrium between flexible tuning fork and a minor conformation, similar, but not identical, to the L-shaped bound conformation. We propose that an open ligand-binding pocket combined with a high conformational penalty for forming the ligand-bound state provide mechanisms for reducing binding affinity while retaining high selectivity.
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Affiliation(s)
- Aiming Ren
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Yi Xue
- Department of Biochemistry and Chemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Alla Peselis
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Alexander Serganov
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Hashim M Al-Hashimi
- Department of Biochemistry and Chemistry, Duke University Medical Center, Durham, NC 27710, USA.
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.
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233
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Regulated Control of the Assembly and Diversity of LPS by Noncoding sRNAs. BIOMED RESEARCH INTERNATIONAL 2015; 2015:153561. [PMID: 26618164 PMCID: PMC4651636 DOI: 10.1155/2015/153561] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 10/07/2015] [Accepted: 10/13/2015] [Indexed: 01/31/2023]
Abstract
The outer membrane (OM) of Gram-negative bacteria is asymmetric due to the presence of lipopolysaccharide (LPS) facing the outer leaflet of the OM and phospholipids facing the periplasmic side. LPS is essential for bacterial viability, since it provides a permeability barrier and is a major virulence determinant in pathogenic bacteria. In Escherichia coli, several steps of LPS biosynthesis and assembly are regulated by the RpoE sigma factor and stress responsive two-component systems as well as dedicated small RNAs. LPS composition is highly heterogeneous and dynamically altered upon stress and other challenges in the environment because of the transcriptional activation of RpoE regulon members and posttranslational control by RpoE-regulated Hfq-dependent RybB and MicA sRNAs. The PhoP/Q two-component system further regulates Kdo2-lipid A modification via MgrR sRNA. Some of these structural alterations are critical for antibiotic resistance, OM integrity, virulence, survival in host, and adaptation to specific environmental niches. The heterogeneity arises following the incorporation of nonstoichiometric modifications in the lipid A part and alterations in the composition of inner and outer core of LPS. The biosynthesis of LPS and phospholipids is tightly coupled. This requires the availability of metabolic precursors, whose accumulation is controlled by sRNAs like SlrA, GlmZ, and GlmY.
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234
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Abstract
Signal sensing in bacteria has traditionally been attributed to protein-based factors. It is however becoming increasingly clear that bacteria also exploit RNAs to serve this role. This review discusses how key developmental processes in bacteria, such as community formation, choice of a sessile versus motile lifestyle, or vegetative growth versus dormant spore formation may be governed by signal sensing RNAs. The signaling molecules that affect these processes, the RNAs that sense these molecules and the underlying molecular basis for specific signal-response are discussed here.
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Affiliation(s)
- Arati Ramesh
- National Center for Biological Sciences, GKVK Campus, Bellary Road, Bangalore 560065, India.
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235
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Yuan X, Khokhani D, Wu X, Yang F, Biener G, Koestler BJ, Raicu V, He C, Waters CM, Sundin GW, Tian F, Yang CH. Cross-talk between a regulatory small RNA, cyclic-di-GMP signalling and flagellar regulator FlhDC for virulence and bacterial behaviours. Environ Microbiol 2015; 17:4745-63. [PMID: 26462993 DOI: 10.1111/1462-2920.13029] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 08/14/2015] [Accepted: 08/15/2015] [Indexed: 12/01/2022]
Abstract
Dickeya dadantii is a globally dispersed phytopathogen which causes diseases on a wide range of host plants. This pathogen utilizes the type III secretion system (T3SS) to suppress host defense responses, and secretes pectate lyase (Pel) to degrade the plant cell wall. Although the regulatory small RNA (sRNA) RsmB, cyclic diguanylate monophosphate (c-di-GMP) and flagellar regulator have been reported to affect the regulation of these two virulence factors or multiple cell behaviours such as motility and biofilm formation, the linkage between these regulatory components that coordinate the cell behaviours remain unclear. Here, we revealed a sophisticated regulatory network that connects the sRNA, c-di-GMP signalling and flagellar master regulator FlhDC. We propose multi-tiered regulatory mechanisms that link the FlhDC to the T3SS through three distinct pathways including the FlhDC-FliA-YcgR3937 pathway; the FlhDC-EcpC-RpoN-HrpL pathway; and the FlhDC-rsmB-RsmA-HrpL pathway. Among these, EcpC is the most dominant factor for FlhDC to positively regulate T3SS expression.
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Affiliation(s)
- Xiaochen Yuan
- Department of Biological Sciences, University of Wisconsin, Milwaukee, WI, 53211, USA
| | - Devanshi Khokhani
- Department of Biological Sciences, University of Wisconsin, Milwaukee, WI, 53211, USA
| | - Xiaogang Wu
- Department of Biological Sciences, University of Wisconsin, Milwaukee, WI, 53211, USA
| | - Fenghuan Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Gabriel Biener
- Department of Physics, University of Wisconsin, Milwaukee, WI, 53211, USA
| | - Benjamin J Koestler
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA
| | - Valerica Raicu
- Department of Biological Sciences, University of Wisconsin, Milwaukee, WI, 53211, USA.,Department of Physics, University of Wisconsin, Milwaukee, WI, 53211, USA
| | - Chenyang He
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Christopher M Waters
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA
| | - George W Sundin
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - Fang Tian
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Ching-Hong Yang
- Department of Biological Sciences, University of Wisconsin, Milwaukee, WI, 53211, USA
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236
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Salmon L, Giambaşu GM, Nikolova EN, Petzold K, Bhattacharya A, Case DA, Al-Hashimi HM. Modulating RNA Alignment Using Directional Dynamic Kinks: Application in Determining an Atomic-Resolution Ensemble for a Hairpin using NMR Residual Dipolar Couplings. J Am Chem Soc 2015; 137:12954-65. [PMID: 26306428 PMCID: PMC4748170 DOI: 10.1021/jacs.5b07229] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Approaches that combine experimental data and computational molecular dynamics (MD) to determine atomic resolution ensembles of biomolecules require the measurement of abundant experimental data. NMR residual dipolar couplings (RDCs) carry rich dynamics information, however, difficulties in modulating overall alignment of nucleic acids have limited the ability to fully extract this information. We present a strategy for modulating RNA alignment that is based on introducing variable dynamic kinks in terminal helices. With this strategy, we measured seven sets of RDCs in a cUUCGg apical loop and used this rich data set to test the accuracy of an 0.8 μs MD simulation computed using the Amber ff10 force field as well as to determine an atomic resolution ensemble. The MD-generated ensemble quantitatively reproduces the measured RDCs, but selection of a sub-ensemble was required to satisfy the RDCs within error. The largest discrepancies between the RDC-selected and MD-generated ensembles are observed for the most flexible loop residues and backbone angles connecting the loop to the helix, with the RDC-selected ensemble resulting in more uniform dynamics. Comparison of the RDC-selected ensemble with NMR spin relaxation data suggests that the dynamics occurs on the ps-ns time scales as verified by measurements of R(1ρ) relaxation-dispersion data. The RDC-satisfying ensemble samples many conformations adopted by the hairpin in crystal structures indicating that intrinsic plasticity may play important roles in conformational adaptation. The approach presented here can be applied to test nucleic acid force fields and to characterize dynamics in diverse RNA motifs at atomic resolution.
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Affiliation(s)
- Loïc Salmon
- Department of Molecular, Cellular, and Developmental Biology and Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - George M. Giambaşu
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, USA
| | - Evgenia N. Nikolova
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Katja Petzold
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | | | - David A. Case
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, USA
| | - Hashim M. Al-Hashimi
- Department of Biochemistry and Chemistry, Duke University School of Medicine, Durham, North Carolina, USA
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237
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Apostolidi M, Saad NY, Drainas D, Pournaras S, Becker HD, Stathopoulos C. A glyS T-box riboswitch with species-specific structural features responding to both proteinogenic and nonproteinogenic tRNAGly isoacceptors. RNA (NEW YORK, N.Y.) 2015; 21:1790-806. [PMID: 26276802 PMCID: PMC4574755 DOI: 10.1261/rna.052712.115] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 07/13/2015] [Indexed: 06/04/2023]
Abstract
In Staphylococcus aureus, a T-box riboswitch exists upstream of the glyS gene to regulate transcription of the sole glycyl-tRNA synthetase, which aminoacylates five tRNA(Gly) isoacceptors bearing GCC or UCC anticodons. Subsequently, the glycylated tRNAs serve as substrates for decoding glycine codons during translation, and also as glycine donors for exoribosomal synthesis of pentaglycine peptides during cell wall formation. Probing of the predicted T-box structure revealed a long stem I, lacking features previously described for similar T-boxes. Moreover, the antiterminator stem includes a 42-nt long intervening sequence, which is staphylococci-specific. Finally, the terminator conformation adopts a rigid two-stem structure, where the intervening sequence forms the first stem followed by the second stem, which includes the more conserved residues. Interestingly, all five tRNA(Gly) isoacceptors interact with S. aureus glyS T-box with different binding affinities and they all induce transcription readthrough at different levels. The ability of both GCC and UCC anticodons to interact with the specifier loop indicates ambiguity during the specifier triplet reading, similar to the unconventional reading of glycine codons during protein synthesis. The S. aureus glyS T-box structure is consistent with the recent crystallographic and NMR studies, despite apparent differences, and highlights the phylogenetic variability of T-boxes when studied in a genome-dependent context. Our data suggest that the S. aureus glyS T-box exhibits differential tRNA selectivity, which possibly contributes toward the regulation and synchronization of ribosomal and exoribosomal peptide synthesis, two essential but metabolically unrelated pathways.
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Affiliation(s)
- Maria Apostolidi
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Nizar Y Saad
- Unité Mixte de Recherche 7156 Génétique Moléculaire, Génomique, Microbiologie, CNRS, Université de Strasbourg, F-67084 Strasbourg, France
| | - Denis Drainas
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Spyros Pournaras
- Department of Microbiology, School of Medicine, University of Athens, 11527 Athens, Greece
| | - Hubert D Becker
- Unité Mixte de Recherche 7156 Génétique Moléculaire, Génomique, Microbiologie, CNRS, Université de Strasbourg, F-67084 Strasbourg, France
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238
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Lussier A, Bastet L, Chauvier A, Lafontaine DA. A kissing loop is important for btuB riboswitch ligand sensing and regulatory control. J Biol Chem 2015; 290:26739-51. [PMID: 26370077 DOI: 10.1074/jbc.m115.684134] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Indexed: 12/18/2022] Open
Abstract
RNA-based genetic regulation is exemplified by metabolite-binding riboswitches that modulate gene expression through conformational changes. Crystal structures show that the Escherichia coli btuB riboswitch contains a kissing loop interaction that is in close proximity to the bound ligand. To analyze the role of the kissing loop interaction in the riboswitch regulatory mechanism, we used RNase H cleavage assays to probe the structure of nascent riboswitch transcripts produced by the E. coli RNA polymerase. By monitoring the folding of the aptamer, kissing loop, and riboswitch expression platform, we established the conformation of each structural component in the absence or presence of bound adenosylcobalamin. We found that the kissing loop interaction is not essential for ligand binding. However, we showed that kissing loop formation improves ligand binding efficiency and is required to couple ligand binding to the riboswitch conformational changes involved in regulating gene expression. These results support a mechanism by which the btuB riboswitch modulates the formation of a tertiary structure to perform metabolite sensing and regulate gene expression.
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Affiliation(s)
- Antony Lussier
- From the Department of Biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, Québec J1K 2R1, Canada
| | - Laurène Bastet
- From the Department of Biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, Québec J1K 2R1, Canada
| | - Adrien Chauvier
- From the Department of Biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, Québec J1K 2R1, Canada
| | - Daniel A Lafontaine
- From the Department of Biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, Québec J1K 2R1, Canada
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239
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FASTR: A novel data format for concomitant representation of RNA sequence and secondary structure information. J Biosci 2015; 40:571-7. [PMID: 26333403 DOI: 10.1007/s12038-015-9546-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Given the importance of RNA secondary structures in defining their biological role, it would be convenient for researchers seeking RNA data if both sequence and structural information pertaining to RNA molecules are made available together. Current nucleotide data repositories archive only RNA sequence data. Furthermore, storage formats which can frugally represent RNA sequence as well as structure data in a single file, are currently unavailable. This article proposes a novel storage format, 'FASTR', for concomitant representation of RNA sequence and structure. The storage efficiency of the proposed FASTR format has been evaluated using RNA data from various microorganisms. Results indicate that the size of FASTR formatted files (containing both RNA sequence as well as structure information) are equivalent to that of FASTA-format files, which contain only RNA sequence information. RNA secondary structure is typically represented using a combination of a string of nucleotide characters along with the corresponding dot-bracket notation indicating structural attributes. 'FASTR' - the novel storage format proposed in the present study enables a frugal representation of both RNA sequence and structural information in the form of a single string. In spite of having a relatively smaller storage footprint, the resultant 'fastr' string(s) retain all sequence as well as secondary structural information that could be stored using a dot-bracket notation. An implementation of the 'FASTR' methodology is available for download at http://metagenomics.atc.tcs.com/compression/fastr.
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240
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Abstract
Next-generation DNA sequencing has revealed the complete genome sequences of numerous organisms, establishing a fundamental and growing understanding of genetic variation and phenotypic diversity. Engineering at the gene, network and whole-genome scale aims to introduce targeted genetic changes both to explore emergent phenotypes and to introduce new functionalities. Expansion of these approaches into massively parallel platforms establishes the ability to generate targeted genome modifications, elucidating causal links between genotype and phenotype, as well as the ability to design and reprogramme organisms. In this Review, we explore techniques and applications in genome engineering, outlining key advances and defining challenges.
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241
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Neuner S, Santner T, Kreutz C, Micura R. The "Speedy" Synthesis of Atom-Specific (15)N Imino/Amido-Labeled RNA. Chemistry 2015; 21:11634-11643. [PMID: 26237536 PMCID: PMC4946632 DOI: 10.1002/chem.201501275] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Although numerous reports on the synthesis of atom-specific (15)N-labeled nucleosides exist, fast and facile access to the corresponding phosphoramidites for RNA solid-phase synthesis is still lacking. This situation represents a severe bottleneck for NMR spectroscopic investigations on functional RNAs. Here, we present optimized procedures to speed up the synthesis of (15)N(1) adenosine and (15)N(1) guanosine amidites, which are the much needed counterparts of the more straightforward-to-achieve (15)N(3) uridine and (15)N(3) cytidine amidites in order to tap full potential of (1)H/(15)N/(15)N-COSY experiments for directly monitoring individual Watson-Crick base pairs in RNA. Demonstrated for two preQ1 riboswitch systems, we exemplify a versatile concept for individual base-pair labeling in the analysis of conformationally flexible RNAs when competing structures and conformational dynamics are encountered.
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Affiliation(s)
- Sandro Neuner
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck (Austria)
| | - Tobias Santner
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck (Austria)
| | - Christoph Kreutz
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck (Austria)
| | - Ronald Micura
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck (Austria)
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242
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Dutta D, Wedekind JE. Gene Regulation Gets in Tune: How Riboswitch Tertiary-Structure Networks Adapt to Meet the Needs of Their Transcription Units. J Mol Biol 2015; 427:3469-3472. [PMID: 26255959 DOI: 10.1016/j.jmb.2015.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Debapratim Dutta
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester NY 14642, USA
| | - Joseph E Wedekind
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester NY 14642, USA.
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243
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Venayak N, Anesiadis N, Cluett WR, Mahadevan R. Engineering metabolism through dynamic control. Curr Opin Biotechnol 2015; 34:142-52. [DOI: 10.1016/j.copbio.2014.12.022] [Citation(s) in RCA: 152] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 12/22/2014] [Accepted: 12/22/2014] [Indexed: 11/30/2022]
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244
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Drory Retwitzer M, Kifer I, Sengupta S, Yakhini Z, Barash D. An Efficient Minimum Free Energy Structure-Based Search Method for Riboswitch Identification Based on Inverse RNA Folding. PLoS One 2015; 10:e0134262. [PMID: 26230932 PMCID: PMC4521916 DOI: 10.1371/journal.pone.0134262] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 07/07/2015] [Indexed: 11/22/2022] Open
Abstract
Riboswitches are RNA genetic control elements that were originally discovered in bacteria and provide a unique mechanism of gene regulation. They work without the participation of proteins and are believed to represent ancient regulatory systems in the evolutionary timescale. One of the biggest challenges in riboswitch research is to find additional eukaryotic riboswitches since more than 20 riboswitch classes have been found in prokaryotes but only one class has been found in eukaryotes. Moreover, this single known class of eukaryotic riboswitch, namely the TPP riboswitch class, has been found in bacteria, archaea, fungi and plants but not in animals. The few examples of eukaryotic riboswitches were identified using sequence-based bioinformatics search methods such as a combination of BLAST and pattern matching techniques that incorporate base-pairing considerations. None of these approaches perform energy minimization structure predictions. There is a clear motivation to develop new bioinformatics methods, aside of the ongoing advances in covariance models, that will sample the sequence search space more flexibly using structural guidance while retaining the computational efficiency of sequence-based methods. We present a new energy minimization approach that transforms structure-based search into a sequence-based search, thereby enabling the utilization of well established sequence-based search utilities such as BLAST and FASTA. The transformation to sequence space is obtained by using an extended inverse RNA folding problem solver with sequence and structure constraints, available within RNAfbinv. Examples in applying the new method are presented for the purine and preQ1 riboswitches. The method is described in detail along with its findings in prokaryotes. Potential uses in finding novel eukaryotic riboswitches and optimizing pre-designed synthetic riboswitches based on ligand simulations are discussed. The method components are freely available for use.
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Affiliation(s)
| | - Ilona Kifer
- Agilent Laboratories, Tel Aviv, Israel; Microsoft R&D Center, Herzliya, Israel
| | - Supratim Sengupta
- Department of Physical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, 741246, India
| | - Zohar Yakhini
- Agilent Laboratories, Tel Aviv, Israel; Laboratory of Computational Biology, Computer Science Department, Israel Institute of Technology, Haifa, 32000, Israel
| | - Danny Barash
- Department of Computer Science, Ben-Gurion University, Beer-Sheva, 84105, Israel
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245
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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: 1.3] [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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246
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Okui S, Kawai G. In NMR tube transcription for rapid screening of RNA conformation. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2015; 34:103-13. [PMID: 25621704 DOI: 10.1080/15257770.2014.964412] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
A simple method for rapid structure screening for RNA by NMR is proposed. Target RNA is transcribed in a NMR tube and its spectra are measured without purification. The proposed method, in NMR tube transcription or INTT, was applied for three RNAs for which NMR spectra have been measured by using the conventionally purified samples. By the real-time measuring, increase of imino proton signals and decrease of NTP signals can be observed. It was confirmed that INTT spectra are in general similar to those obtained by the conventional method. INTT can be used for the first-step screening of RNA folding.
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Affiliation(s)
- Saya Okui
- a Department of Life and Environmental Sciences, Faculty of Engineering , Chiba Institute of Technology , Narashino , Chiba , Japan
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247
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Novel riboswitch-binding flavin analog that protects mice against Clostridium difficile infection without inhibiting cecal flora. Antimicrob Agents Chemother 2015; 59:5736-46. [PMID: 26169403 DOI: 10.1128/aac.01282-15] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 07/03/2015] [Indexed: 01/08/2023] Open
Abstract
Novel mechanisms of action and new chemical scaffolds are needed to rejuvenate antibacterial drug discovery, and riboswitch regulators of bacterial gene expression are a promising class of targets for the discovery of new leads. Herein, we report the characterization of 5-(3-(4-fluorophenyl)butyl)-7,8-dimethylpyrido[3,4-b]quinoxaline-1,3(2H,5H)-dione (5FDQD)-an analog of riboflavin that was designed to bind riboswitches that naturally recognize the essential coenzyme flavin mononucleotide (FMN) and regulate FMN and riboflavin homeostasis. In vitro, 5FDQD and FMN bind to and trigger the function of an FMN riboswitch with equipotent activity. MIC and time-kill studies demonstrated that 5FDQD has potent and rapidly bactericidal activity against Clostridium difficile. In C57BL/6 mice, 5FDQD completely prevented the onset of lethal antibiotic-induced C. difficile infection (CDI). Against a panel of bacteria representative of healthy bowel flora, the antibacterial selectivity of 5FDQD was superior to currently marketed CDI therapeutics, with very little activity against representative strains from the Bacteroides, Lactobacillus, Bifidobacterium, Actinomyces, and Prevotella genera. Accordingly, a single oral dose of 5FDQD caused less alteration of culturable cecal flora in mice than the comparators. Collectively, these data suggest that 5FDQD or closely related analogs could potentially provide a high rate of CDI cure with a low likelihood of infection recurrence. Future studies will seek to assess the role of FMN riboswitch binding to the mechanism of 5FDQD antibacterial action. In aggregate, our results indicate that riboswitch-binding antibacterial compounds can be discovered and optimized to exhibit activity profiles that merit preclinical and clinical development as potential antibacterial therapeutic agents.
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248
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Wunderlich CH, Juen MA, LeBlanc RM, Longhini AP, Dayie TK, Kreutz C. Stable isotope-labeled RNA phosphoramidites to facilitate dynamics by NMR. Methods Enzymol 2015; 565:461-94. [PMID: 26577742 DOI: 10.1016/bs.mie.2015.06.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Given that Ribonucleic acids (RNAs) are a central hub of various cellular processes, methods to synthesize these RNAs for biophysical studies are much needed. Here, we showcase the applicability of 6-(13)C-pyrimidine phosphoramidites to introduce isolated (13)C-(1)H spin pairs into RNAs up to 40 nucleotides long. The method allows the incorporation of 6-(13)C-uridine and -cytidine residues at any desired position within a target RNA. By site-specific positioning of the (13)C-label using RNA solid phase synthesis, these stable isotope-labeling patterns are especially well suited to resolve resonance assignment ambiguities. Of even greater importance, the labeling pattern affords accurate quantification of important functional transitions of biologically relevant RNAs (e.g., riboswitch aptamer domains, viral RNAs, or ribozymes) in the μs- to ms time regime and beyond without complications of one bond carbon scalar couplings. We outline the chemical synthesis of the 6-(13)C-pyrimidine building blocks and their use in RNA solid phase synthesis and demonstrate their utility in Carr Purcell Meiboom Gill relaxation dispersion, ZZ exchange, and chemical exchange saturation transfer NMR experiments.
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Affiliation(s)
- Christoph H Wunderlich
- Institute of Organic Chemistry and Center for Biomolecular Sciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Michael A Juen
- Institute of Organic Chemistry and Center for Biomolecular Sciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Regan M LeBlanc
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, Maryland, USA
| | - Andrew P Longhini
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, Maryland, USA
| | - T Kwaku Dayie
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, Maryland, USA.
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Biomolecular Sciences Innsbruck, University of Innsbruck, Innsbruck, Austria.
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249
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Peselis A, Gao A, Serganov A. Cooperativity, allostery and synergism in ligand binding to riboswitches. Biochimie 2015; 117:100-9. [PMID: 26143008 DOI: 10.1016/j.biochi.2015.06.028] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 06/29/2015] [Indexed: 01/04/2023]
Abstract
Recent progress in identification and characterization of novel types of non-coding RNAs has proven that RNAs carry out a variety of cellular functions ranging from scaffolding to gene expression control. In both prokaryotic and eukaryotic cells, several classes of non-coding RNAs control expression of dozens of genes in response to specific cues. One of the most interesting and outstanding questions in the RNA field is whether regulatory RNAs are capable of employing basic biological concepts, such as allostery and cooperativity, previously attributed to the function of proteins. Aside from regulatory RNAs that form complementary base pairing with their nucleic acid targets, several RNA classes modulate gene expression via molecular mechanisms which can be paralleled to protein-mediated regulation. Among these RNAs are riboswitches, metabolite-sensing non-coding regulatory elements that adopt intrinsic three-dimensional structures and specifically bind various small molecule ligands. These characteristics of riboswitches make them well-suited for complex regulatory responses observed in allosteric and cooperative protein systems. Here we present an overview of the biochemical, genetic, and structural studies of riboswitches with a major focus on complex regulatory mechanisms and biological principles utilized by riboswitches for such genetic modulation.
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Affiliation(s)
- Alla Peselis
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA
| | - Ang Gao
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA
| | - Alexander Serganov
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA.
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250
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Duss O, Diarra Dit Konté N, Allain FHT. Cut and paste RNA for nuclear magnetic resonance, paramagnetic resonance enhancement, and electron paramagnetic resonance structural studies. Methods Enzymol 2015; 565:537-62. [PMID: 26577744 DOI: 10.1016/bs.mie.2015.05.029] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
RNA is a crucial regulator involved in most molecular processes of life. Understanding its function at the molecular level requires high-resolution structural information. However, the dynamic nature of RNA complicates structure determination because crystallization is often not possible or can result in crystal-packing artifacts resulting in nonnative structures. To study RNA and its complexes in solution, we described an approach in which large multi-domain RNA or protein-RNA complex structures can be determined at high resolution from isolated domains determined by nuclear magnetic resonance (NMR) spectroscopy, and then constructing the entire macromolecular structure using electron paramagnetic resonance (EPR) long-range distance constraints. Every step in this structure determination approach requires different types of isotope or spin-labeled RNAs. Here, we present a simple modular RNA cut and paste approach including protocols to generate (1) small isotopically labeled RNAs (<10 nucleotides) for NMR structural studies, which cannot be obtained by standard protocols, (2) large segmentally isotope and/or spin-labeled RNAs for diamagnetic NMR and paramagnetic relaxation enhancement NMR, and (3) large spin-labeled RNAs for pulse EPR spectroscopy.
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Affiliation(s)
- Olivier Duss
- Institute for Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland.
| | | | - Frédéric H-T Allain
- Institute for Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland.
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