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Koksaldi I, Park D, Atilla A, Kang H, Kim J, Seker UOS. RNA-Based Sensor Systems for Affordable Diagnostics in the Age of Pandemics. ACS Synth Biol 2024; 13:1026-1037. [PMID: 38588603 PMCID: PMC11036506 DOI: 10.1021/acssynbio.3c00698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 03/25/2024] [Accepted: 03/25/2024] [Indexed: 04/10/2024]
Abstract
In the era of the COVID-19 pandemic, the significance of point-of-care (POC) diagnostic tools has become increasingly vital, driven by the need for quick and precise virus identification. RNA-based sensors, particularly toehold sensors, have emerged as promising candidates for POC detection systems due to their selectivity and sensitivity. Toehold sensors operate by employing an RNA switch that changes the conformation when it binds to a target RNA molecule, resulting in a detectable signal. This review focuses on the development and deployment of RNA-based sensors for POC viral RNA detection with a particular emphasis on toehold sensors. The benefits and limits of toehold sensors are explored, and obstacles and future directions for improving their performance within POC detection systems are presented. The use of RNA-based sensors as a technology for rapid and sensitive detection of viral RNA holds great potential for effectively managing (dealing/coping) with present and future pandemics in resource-constrained settings.
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Affiliation(s)
- Ilkay
Cisil Koksaldi
- UNAM
− Institute of Materials Science and Nanotechnology, National
Nanotechnology Research Center (UNAM), Bilkent
University, Ankara 06800, Turkey
| | - Dongwon Park
- Department
of Life Sciences, Pohang University of Science
and Technology, Pohang 37673, South Korea
| | - Abdurahman Atilla
- UNAM
− Institute of Materials Science and Nanotechnology, National
Nanotechnology Research Center (UNAM), Bilkent
University, Ankara 06800, Turkey
| | - Hansol Kang
- Department
of Life Sciences, Pohang University of Science
and Technology, Pohang 37673, South Korea
| | - Jongmin Kim
- Department
of Life Sciences, Pohang University of Science
and Technology, Pohang 37673, South Korea
| | - Urartu Ozgur Safak Seker
- UNAM
− Institute of Materials Science and Nanotechnology, National
Nanotechnology Research Center (UNAM), Bilkent
University, Ankara 06800, Turkey
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2
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Lu Y, Lee J, Li J, Allu SR, Wang J, Kim H, Bullaughey KL, Fisher SA, Nordgren CE, Rosario JG, Anderson SA, Ulyanova AV, Brem S, Chen HI, Wolf JA, Grady MS, Vinogradov SA, Kim J, Eberwine J. CHEX-seq detects single-cell genomic single-stranded DNA with catalytical potential. Nat Commun 2023; 14:7346. [PMID: 37963886 PMCID: PMC10645931 DOI: 10.1038/s41467-023-43158-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 11/02/2023] [Indexed: 11/16/2023] Open
Abstract
Genomic DNA (gDNA) undergoes structural interconversion between single- and double-stranded states during transcription, DNA repair and replication, which is critical for cellular homeostasis. We describe "CHEX-seq" which identifies the single-stranded DNA (ssDNA) in situ in individual cells. CHEX-seq uses 3'-terminal blocked, light-activatable probes to prime the copying of ssDNA into complementary DNA that is sequenced, thereby reporting the genome-wide single-stranded chromatin landscape. CHEX-seq is benchmarked in human K562 cells, and its utilities are demonstrated in cultures of mouse and human brain cells as well as immunostained spatially localized neurons in brain sections. The amount of ssDNA is dynamically regulated in response to perturbation. CHEX-seq also identifies single-stranded regions of mitochondrial DNA in single cells. Surprisingly, CHEX-seq identifies single-stranded loci in mouse and human gDNA that catalyze porphyrin metalation in vitro, suggesting a catalytic activity for genomic ssDNA. We posit that endogenous DNA enzymatic activity is a function of genomic ssDNA.
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Affiliation(s)
- Youtao Lu
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jaehee Lee
- Department of Systems Pharmacology and Translational Therapeutics Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jifen Li
- Department of Systems Pharmacology and Translational Therapeutics Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Srinivasa Rao Allu
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jinhui Wang
- Department of Systems Pharmacology and Translational Therapeutics Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - HyunBum Kim
- Department of Systems Pharmacology and Translational Therapeutics Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kevin L Bullaughey
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Stephen A Fisher
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - C Erik Nordgren
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jean G Rosario
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Stewart A Anderson
- Department of Psychiatry, Children's Hospital of Philadelphia, ARC 517, 3615 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Alexandra V Ulyanova
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Steven Brem
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - H Isaac Chen
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - John A Wolf
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - M Sean Grady
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Sergei A Vinogradov
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Junhyong Kim
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - James Eberwine
- Department of Systems Pharmacology and Translational Therapeutics Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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3
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Assmann SM, Chou HL, Bevilacqua PC. Rock, scissors, paper: How RNA structure informs function. THE PLANT CELL 2023; 35:1671-1707. [PMID: 36747354 DOI: 10.1093/plcell/koad026] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 01/05/2023] [Accepted: 01/30/2023] [Indexed: 05/30/2023]
Abstract
RNA can fold back on itself to adopt a wide range of structures. These range from relatively simple hairpins to intricate 3D folds and can be accompanied by regulatory interactions with both metabolites and macromolecules. The last 50 yr have witnessed elucidation of an astonishing array of RNA structures including transfer RNAs, ribozymes, riboswitches, the ribosome, the spliceosome, and most recently entire RNA structuromes. These advances in RNA structural biology have deepened insight into fundamental biological processes including gene editing, transcription, translation, and structure-based detection and response to temperature and other environmental signals. These discoveries reveal that RNA can be relatively static, like a rock; that it can have catalytic functions of cutting bonds, like scissors; and that it can adopt myriad functional shapes, like paper. We relate these extraordinary discoveries in the biology of RNA structure to the plant way of life. We trace plant-specific discovery of ribozymes and riboswitches, alternative splicing, organellar ribosomes, thermometers, whole-transcriptome structuromes and pan-structuromes, and conclude that plants have a special set of RNA structures that confer unique types of gene regulation. We finish with a consideration of future directions for the RNA structure-function field.
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Affiliation(s)
- Sarah M Assmann
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Hong-Li Chou
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Philip C Bevilacqua
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
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4
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Yu-Nan H, Kang W, Yu S, Xiao-Jun X, Yan W, Xing-Ao L, Ting-Ting S. Molecular dynamics simulation on the Thermosinus carboxydivorans pfl ZTP riboswitch by ligand binding. Biochem Biophys Res Commun 2022; 627:184-190. [PMID: 36044800 DOI: 10.1016/j.bbrc.2022.08.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/03/2022] [Accepted: 08/11/2022] [Indexed: 12/01/2022]
Abstract
Riboswitches are RNA molecules that can regulate gene expression which is affected by ligand-binding during cotranscriptional folding process. However, the role of ligand during the folding is still unclear. In this study, the pfl domain of Thermosinus carboxydivorans ZTP riboswitch was discussed. The ligand is molecule ZMP. We mainly analyzed the change of ZMP-free and ZMP-bound aptamer domain by the dynamics simulation method. Structural features by calculating their RMSD, RMSF, etc. are analyzed. The results demonstrate that the binding domain require the presence of ZMP to maintain a stable fold. It also suggested that ZMP specificly binding to ZTP can generate more hydrogen bonds in the binding domain. Through the calculation of binding free energy decomposition of each nucleotide, molecule ZMP was found to promote the recognition and binding process of ligands by controlling some special nucleotides in the process of ligand binding. At last, the dynamical correlation and components of conformational motions were both applied to explore the effect of molecule ZMP to ZTP riboswitch. In general, ZMP can effectively affect the motions of the pfl riboswitch and facilitate the folding process of the ZTP riboswitch.These results may provide some new ideas for structural changes in riboswitches and their cotranscriptional folding process.
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Affiliation(s)
- He Yu-Nan
- Department of Physics, Zhejiang University of Science and Technology, Hangzhou, Zhejiang, 310008, PR China
| | - Wang Kang
- Department of Physics, Zhejiang University of Science and Technology, Hangzhou, Zhejiang, 310008, PR China
| | - Shen Yu
- Department of Physics, Zhejiang University of Science and Technology, Hangzhou, Zhejiang, 310008, PR China
| | - Xu Xiao-Jun
- Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou, Jiangsu, 213001, PR China
| | - Wang Yan
- Department of Physics, Zhejiang University of Science and Technology, Hangzhou, Zhejiang, 310008, PR China
| | - Li Xing-Ao
- Department of Physics, Zhejiang University of Science and Technology, Hangzhou, Zhejiang, 310008, PR China.
| | - Sun Ting-Ting
- Department of Physics, Zhejiang University of Science and Technology, Hangzhou, Zhejiang, 310008, PR China.
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5
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Peng H, Latifi B, Müller S, Lupták A, Chen IA. Self-cleaving ribozymes: substrate specificity and synthetic biology applications. RSC Chem Biol 2021; 2:1370-1383. [PMID: 34704043 PMCID: PMC8495972 DOI: 10.1039/d0cb00207k] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 06/14/2021] [Indexed: 12/22/2022] Open
Abstract
Various self-cleaving ribozymes appearing in nature catalyze the sequence-specific intramolecular cleavage of RNA and can be engineered to catalyze cleavage of appropriate substrates in an intermolecular fashion, thus acting as true catalysts. The mechanisms of the small, self-cleaving ribozymes have been extensively studied and reviewed previously. Self-cleaving ribozymes can possess high catalytic activity and high substrate specificity; however, substrate specificity is also engineerable within the constraints of the ribozyme structure. While these ribozymes share a common fundamental catalytic mechanism, each ribozyme family has a unique overall architecture and active site organization, indicating that several distinct structures yield this chemical activity. The multitude of catalytic structures, combined with some flexibility in substrate specificity within each family, suggests that such catalytic RNAs, taken together, could access a wide variety of substrates. Here, we give an overview of 10 classes of self-cleaving ribozymes and capture what is understood about their substrate specificity and synthetic applications. Evolution of these ribozymes in an RNA world might be characterized by the emergence of a new ribozyme family followed by rapid adaptation or diversification for specific substrates. Self-cleaving ribozymes have become important tools of synthetic biology. Here we summarize the substrate specificity and applications of the main classes of these ribozymes.![]()
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Affiliation(s)
- Huan Peng
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles CA 90095 USA
| | - Brandon Latifi
- Department of Pharmaceutical Sciences, University of California Irvine CA 92697 USA
| | - Sabine Müller
- Institute for Biochemistry, University Greifswald 17487 Greifswald Germany
| | - Andrej Lupták
- Department of Pharmaceutical Sciences, University of California Irvine CA 92697 USA
| | - Irene A Chen
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles CA 90095 USA
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6
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Ma L, Huang Z, Liu J. Selection of a self-cleaving ribozyme activated in a chemically and thermally denaturing environment. Chem Commun (Camb) 2021; 57:7641-7644. [PMID: 34250983 DOI: 10.1039/d1cc03102c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A new self-cleaving ribozyme was obtained from in vitro selection, displaying site-specific cleavage activity under denaturing conditions, such as high temperatures up to 95 °C, and denaturing solvents (20 M formamide). Adding salt such as Mg2+ also inhibited its activity. The conserved ribozyme sequence was found in the genome of several extremophiles, suggesting its potential biological relevance. This study provides an example of a ribozyme working under exotic conditions, which may expand the application of ribozymes in non-biological environments.
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Affiliation(s)
- Lingzi Ma
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.
| | - Zhicheng Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.
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7
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Zhou T, Wang H, Song L, Zhao Y. Computational study of switching mechanism in add A-riboswitch. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2020. [DOI: 10.1142/s0219633620400015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Riboswitch can bind small molecules to regulate gene expression. Unlike other RNAs, riboswitch relies on its conformational switching for regulation. However, the understanding of the switching mechanism is still limited. Here, we focussed on the add A-riboswitch to illustrate the dynamical switching mechanism as an example. We performed molecular dynamics simulation, conservation and co-evolution calculations to infer the dynamical motions and evolutionary base pairings. The results suggest that the binding domain is stable for molecule recognition and binding, whereas the switching base pairings are co-evolutionary for translation. The understanding of the add A-riboswitch switching mechanism provides a potential solution for riboswitch drug design.
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Affiliation(s)
- Ting Zhou
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan 430079, P. R. China
| | - Huiwen Wang
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan 430079, P. R. China
| | - Linlu Song
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan 430079, P. R. China
| | - Yunjie Zhao
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan 430079, P. R. China
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8
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Ma L, Liu J. Catalytic Nucleic Acids: Biochemistry, Chemical Biology, Biosensors, and Nanotechnology. iScience 2020; 23:100815. [PMID: 31954323 PMCID: PMC6962706 DOI: 10.1016/j.isci.2019.100815] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/11/2019] [Accepted: 12/26/2019] [Indexed: 01/06/2023] Open
Abstract
Since the initial discovery of ribozymes in the early 1980s, catalytic nucleic acids have been used in different areas. Compared with protein enzymes, catalytic nucleic acids are programmable in structure, easy to modify, and more stable especially for DNA. We take a historic view to summarize a few main interdisciplinary areas of research on nucleic acid enzymes that may have broader impacts. Early efforts on ribozymes in the 1980s have broken the notion that all enzymes are proteins, supplying new evidence for the RNA world hypothesis. In 1994, the first catalytic DNA (DNAzyme) was reported. Since 2000, the biosensor applications of DNAzymes have emerged and DNAzymes are particularly useful for detecting metal ions, a challenging task for enzymes and antibodies. Combined with nanotechnology, DNAzymes are key building elements for switches allowing dynamic control of materials assembly. The search for new DNAzymes and ribozymes is facilitated by developments in DNA sequencing and computational algorithms, further broadening our fundamental understanding of their biochemistry.
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Affiliation(s)
- Lingzi Ma
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada.
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9
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Weinberg CE, Weinberg Z, Hammann C. Novel ribozymes: discovery, catalytic mechanisms, and the quest to understand biological function. Nucleic Acids Res 2019; 47:9480-9494. [PMID: 31504786 PMCID: PMC6765202 DOI: 10.1093/nar/gkz737] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 08/08/2019] [Accepted: 08/21/2019] [Indexed: 12/21/2022] Open
Abstract
Small endonucleolytic ribozymes promote the self-cleavage of their own phosphodiester backbone at a specific linkage. The structures of and the reactions catalysed by members of individual families have been studied in great detail in the past decades. In recent years, bioinformatics studies have uncovered a considerable number of new examples of known catalytic RNA motifs. Importantly, entirely novel ribozyme classes were also discovered, for most of which both structural and biochemical information became rapidly available. However, for the majority of the new ribozymes, which are found in the genomes of a variety of species, a biological function remains elusive. Here, we concentrate on the different approaches to find catalytic RNA motifs in sequence databases. We summarize the emerging principles of RNA catalysis as observed for small endonucleolytic ribozymes. Finally, we address the biological functions of those ribozymes, where relevant information is available and common themes on their cellular activities are emerging. We conclude by speculating on the possibility that the identification and characterization of proteins that we hypothesize to be endogenously associated with catalytic RNA might help in answering the ever-present question of the biological function of the growing number of genomically encoded, small endonucleolytic ribozymes.
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Affiliation(s)
- Christina E Weinberg
- Institute for Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany
| | - Zasha Weinberg
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Centre for Bioinformatics, Leipzig University, Härtelstraße 16–18, 04107 Leipzig, Germany
| | - Christian Hammann
- Ribogenetics & Biochemistry, Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany
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10
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Intracellular Imaging with Genetically Encoded RNA-based Molecular Sensors. NANOMATERIALS 2019; 9:nano9020233. [PMID: 30744040 PMCID: PMC6410142 DOI: 10.3390/nano9020233] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 02/05/2019] [Accepted: 02/05/2019] [Indexed: 01/10/2023]
Abstract
Genetically encodable sensors have been widely used in the detection of intracellular molecules ranging from metal ions and metabolites to nucleic acids and proteins. These biosensors are capable of monitoring in real-time the cellular levels, locations, and cell-to-cell variations of the target compounds in living systems. Traditionally, the majority of these sensors have been developed based on fluorescent proteins. As an exciting alternative, genetically encoded RNA-based molecular sensors (GERMS) have emerged over the past few years for the intracellular imaging and detection of various biological targets. In view of their ability for the general detection of a wide range of target analytes, and the modular and simple design principle, GERMS are becoming a popular choice for intracellular analysis. In this review, we summarize different design principles of GERMS based on various RNA recognition modules, transducer modules, and reporting systems. Some recent advances in the application of GERMS for intracellular imaging are also discussed. With further improvement in biostability, sensitivity, and robustness, GERMS can potentially be widely used in cell biology and biotechnology.
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11
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Churkin A, Retwitzer MD, Reinharz V, Ponty Y, Waldispühl J, Barash D. Design of RNAs: comparing programs for inverse RNA folding. Brief Bioinform 2018; 19:350-358. [PMID: 28049135 PMCID: PMC6018860 DOI: 10.1093/bib/bbw120] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Computational programs for predicting RNA sequences with desired folding properties have been extensively developed and expanded in the past several years. Given a secondary structure, these programs aim to predict sequences that fold into a target minimum free energy secondary structure, while considering various constraints. This procedure is called inverse RNA folding. Inverse RNA folding has been traditionally used to design optimized RNAs with favorable properties, an application that is expected to grow considerably in the future in light of advances in the expanding new fields of synthetic biology and RNA nanostructures. Moreover, it was recently demonstrated that inverse RNA folding can successfully be used as a valuable preprocessing step in computational detection of novel noncoding RNAs. This review describes the most popular freeware programs that have been developed for such purposes, starting from RNAinverse that was devised when formulating the inverse RNA folding problem. The most recently published ones that consider RNA secondary structure as input are antaRNA, RNAiFold and incaRNAfbinv, each having different features that could be beneficial to specific biological problems in practice. The various programs also use distinct approaches, ranging from ant colony optimization to constraint programming, in addition to adaptive walk, simulated annealing and Boltzmann sampling. This review compares between the various programs and provides a simple description of the various possibilities that would benefit practitioners in selecting the most suitable program. It is geared for specific tasks requiring RNA design based on input secondary structure, with an outlook toward the future of RNA design programs.
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Affiliation(s)
- Alexander Churkin
- Shamoon College of Engineering and Physics Department at Ben-Gurion University, Beer-Sheva, Israel
| | | | - Vladimir Reinharz
- Department of Computer Science, Ben-Gurion University, Beer-Sheva, Israel
- School of Computer Science, McGill University, Montréal QC, Canada
| | - Yann Ponty
- Laboratoire d’informatique, École Polytechnique, Palaiseau, France
| | | | - Danny Barash
- Department of Computer Science, Ben-Gurion University, Beer-Sheva, Israel
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12
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Antunes D, Jorge NAN, Caffarena ER, Passetti F. Using RNA Sequence and Structure for the Prediction of Riboswitch Aptamer: A Comprehensive Review of Available Software and Tools. Front Genet 2018; 8:231. [PMID: 29403526 PMCID: PMC5780412 DOI: 10.3389/fgene.2017.00231] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 12/21/2017] [Indexed: 12/14/2022] Open
Abstract
RNA molecules are essential players in many fundamental biological processes. Prokaryotes and eukaryotes have distinct RNA classes with specific structural features and functional roles. Computational prediction of protein structures is a research field in which high confidence three-dimensional protein models can be proposed based on the sequence alignment between target and templates. However, to date, only a few approaches have been developed for the computational prediction of RNA structures. Similar to proteins, RNA structures may be altered due to the interaction with various ligands, including proteins, other RNAs, and metabolites. A riboswitch is a molecular mechanism, found in the three kingdoms of life, in which the RNA structure is modified by the binding of a metabolite. It can regulate multiple gene expression mechanisms, such as transcription, translation initiation, and mRNA splicing and processing. Due to their nature, these entities also act on the regulation of gene expression and detection of small metabolites and have the potential to helping in the discovery of new classes of antimicrobial agents. In this review, we describe software and web servers currently available for riboswitch aptamer identification and secondary and tertiary structure prediction, including applications.
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Affiliation(s)
- Deborah Antunes
- Scientific Computing Program (PROCC), Computational Biophysics and Molecular Modeling Group, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Natasha A N Jorge
- Laboratory of Functional Genomics and Bioinformatics, Oswaldo Cruz Institute, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.,Laboratory of Gene Expression Regulation, Carlos Chagas Institute, Fundação Oswaldo Cruz, Curitiba, Brazil
| | - Ernesto R Caffarena
- Scientific Computing Program (PROCC), Computational Biophysics and Molecular Modeling Group, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Fabio Passetti
- Laboratory of Functional Genomics and Bioinformatics, Oswaldo Cruz Institute, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.,Laboratory of Gene Expression Regulation, Carlos Chagas Institute, Fundação Oswaldo Cruz, Curitiba, Brazil
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13
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de la Peña M, García-Robles I, Cervera A. The Hammerhead Ribozyme: A Long History for a Short RNA. Molecules 2017; 22:molecules22010078. [PMID: 28054987 PMCID: PMC6155905 DOI: 10.3390/molecules22010078] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 12/28/2016] [Accepted: 12/29/2016] [Indexed: 01/22/2023] Open
Abstract
Small nucleolytic ribozymes are a family of naturally occurring RNA motifs that catalyse a self-transesterification reaction in a highly sequence-specific manner. The hammerhead ribozyme was the first reported and the most extensively studied member of this family. However, and despite intense biochemical and structural research for three decades since its discovery, the history of this model ribozyme seems to be far from finished. The hammerhead ribozyme has been regarded as a biological oddity typical of small circular RNA pathogens of plants. More recently, numerous and new variations of this ribozyme have been found to inhabit the genomes of organisms from all life kingdoms, although their precise biological functions are not yet well understood.
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Affiliation(s)
- Marcos de la Peña
- Instituto de Biología Molecular y Celular de Plantas (IBMCP) (CSIC-UPV), C/Ingeniero Fausto Elio s/n, 46022 Valencia, Spain.
| | - Inmaculada García-Robles
- Department of Genetics, University of Valencia, C/Dr. Moliner 50, Burjassot, 46100 Valencia, Spain.
| | - Amelia Cervera
- Instituto de Biología Molecular y Celular de Plantas (IBMCP) (CSIC-UPV), C/Ingeniero Fausto Elio s/n, 46022 Valencia, Spain.
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14
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Drory Retwitzer M, Reinharz V, Ponty Y, Waldispühl J, Barash D. incaRNAfbinv: a web server for the fragment-based design of RNA sequences. Nucleic Acids Res 2016; 44:W308-14. [PMID: 27185893 PMCID: PMC5741205 DOI: 10.1093/nar/gkw440] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 05/06/2016] [Indexed: 01/02/2023] Open
Abstract
In recent years, new methods for computational RNA design have been developed and applied to various problems in synthetic biology and nanotechnology. Lately, there is considerable interest in incorporating essential biological information when solving the inverse RNA folding problem. Correspondingly, RNAfbinv aims at including biologically meaningful constraints and is the only program to-date that performs a fragment-based design of RNA sequences. In doing so it allows the design of sequences that do not necessarily exactly fold into the target, as long as the overall coarse-grained tree graph shape is preserved. Augmented by the weighted sampling algorithm of incaRNAtion, our web server called incaRNAfbinv implements the method devised in RNAfbinv and offers an interactive environment for the inverse folding of RNA using a fragment-based design approach. It takes as input: a target RNA secondary structure; optional sequence and motif constraints; optional target minimum free energy, neutrality and GC content. In addition to the design of synthetic regulatory sequences, it can be used as a pre-processing step for the detection of novel natural occurring RNAs. The two complementary methodologies RNAfbinv and incaRNAtion are merged together and fully implemented in our web server incaRNAfbinv, available at http://www.cs.bgu.ac.il/incaRNAfbinv.
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Affiliation(s)
| | - Vladimir Reinharz
- School of Computer Science & McGill Centre for Bioinformatics, McGill University, Montréal, QC H3A 0E9, Canada
| | - Yann Ponty
- Laboratoire d'Informatique (LIX)-CNRS UMR 7161, École Polytechnique, 91128 Palaiseau, France AMIB team/project, INRIA Saclay, Bâtiment Alan Turing, 91128 Palaiseau, France
| | - Jérôme Waldispühl
- School of Computer Science & McGill Centre for Bioinformatics, McGill University, Montréal, QC H3A 0E9, Canada
| | - Danny Barash
- Department of Computer Science, Ben-Gurion University, Beer-Sheva 84105, Israel
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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: 1.1] [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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Drory Retwitzer M, Polishchuk M, Churkin E, Kifer I, Yakhini Z, Barash D. RNAPattMatch: a web server for RNA sequence/structure motif detection based on pattern matching with flexible gaps. Nucleic Acids Res 2015; 43:W507-12. [PMID: 25940619 PMCID: PMC4489251 DOI: 10.1093/nar/gkv435] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 04/23/2015] [Indexed: 11/13/2022] Open
Abstract
Searching for RNA sequence-structure patterns is becoming an essential tool for RNA practitioners. Novel discoveries of regulatory non-coding RNAs in targeted organisms and the motivation to find them across a wide range of organisms have prompted the use of computational RNA pattern matching as an enhancement to sequence similarity. State-of-the-art programs differ by the flexibility of patterns allowed as queries and by their simplicity of use. In particular-no existing method is available as a user-friendly web server. A general program that searches for RNA sequence-structure patterns is RNA Structator. However, it is not available as a web server and does not provide the option to allow flexible gap pattern representation with an upper bound of the gap length being specified at any position in the sequence. Here, we introduce RNAPattMatch, a web-based application that is user friendly and makes sequence/structure RNA queries accessible to practitioners of various background and proficiency. It also extends RNA Structator and allows a more flexible variable gaps representation, in addition to analysis of results using energy minimization methods. RNAPattMatch service is available at http://www.cs.bgu.ac.il/rnapattmatch. A standalone version of the search tool is also available to download at the site.
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Affiliation(s)
| | - Maya Polishchuk
- Department of Computer Science, Ben-Gurion University, Beer-Sheva 84105, Israel Department of Computational Biology, Vavilov Institute of General Genetics, Russian Academy of Science, Moscow 11933, Russia
| | - Elena Churkin
- Department of Computer Science, Ben-Gurion University, Beer-Sheva 84105, Israel
| | - Ilona Kifer
- Agilent Laboratories, Agilent Technologies, Tel Aviv 49527, Israel Microsoft R&D Center, Herzliya 46725 , Israel
| | - Zohar Yakhini
- Agilent Laboratories, Agilent Technologies, Tel Aviv 49527, 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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Yadav S, Swati D, Chandrasekharan H. Thiamine Pyrophosphate Riboswitch in Some Representative Plant Species: A Bioinformatics Study. J Comput Biol 2015; 22:1-9. [DOI: 10.1089/cmb.2014.0169] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Sunita Yadav
- Department of Bioinformatics, MMV, Banaras Hindu University, Varanasi, India
| | - D. Swati
- Department of Bioinformatics, MMV, Banaras Hindu University, Varanasi, India
- Department of Physics, MMV, Banaras Hindu University, Varanasi, India
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18
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Witzany G. RNA sociology: group behavioral motifs of RNA consortia. Life (Basel) 2014; 4:800-18. [PMID: 25426799 PMCID: PMC4284468 DOI: 10.3390/life4040800] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 11/11/2014] [Accepted: 11/12/2014] [Indexed: 02/07/2023] Open
Abstract
RNA sociology investigates the behavioral motifs of RNA consortia from the social science perspective. Besides the self-folding of RNAs into single stem loop structures, group building of such stem loops results in a variety of essential agents that are highly active in regulatory processes in cellular and non-cellular life. RNA stem loop self-folding and group building do not depend solely on sequence syntax; more important are their contextual (functional) needs. Also, evolutionary processes seem to occur through RNA stem loop consortia that may act as a complement. This means the whole entity functions only if all participating parts are coordinated, although the complementary building parts originally evolved for different functions. If complementary groups, such as rRNAs and tRNAs, are placed together in selective pressure contexts, new evolutionary features may emerge. Evolution initiated by competent agents in natural genome editing clearly contrasts with statistical error replication narratives.
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Affiliation(s)
- Guenther Witzany
- Telos-Philosophische Praxis, Vogelsangstraße 18c, 5111-Buermoos, Austria.
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Vazquez-Anderson J, Contreras LM. Regulatory RNAs: charming gene management styles for synthetic biology applications. RNA Biol 2013; 10:1778-97. [PMID: 24356572 DOI: 10.4161/rna.27102] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
RNAs have many important functional properties, including that they are independently controllable and highly tunable. As a result of these advantageous properties, their use in a myriad of sophisticated devices has been widely explored. Yet, the exploitation of RNAs for synthetic applications is highly dependent on the ability to characterize the many new molecules that continue to be discovered by large-scale sequencing and high-throughput screening techniques. In this review, we present an exhaustive survey of the most recent synthetic bacterial riboswitches and small RNAs while emphasizing their virtues in gene expression management. We also explore the use of these RNA components as building blocks in the RNA synthetic biology toolbox and discuss examples of synthetic RNA components used to rewire bacterial regulatory circuitry. We anticipate that this field will expand its catalog of smart devices by mimicking and manipulating natural RNA mechanisms and functions.
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Affiliation(s)
- Jorge Vazquez-Anderson
- McKetta Department of Chemical Engineering; University of Texas at Austin; Austin, TX USA
| | - Lydia M Contreras
- McKetta Department of Chemical Engineering; University of Texas at Austin; Austin, TX USA
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Abstract
A key step toward understanding a metagenomics data set is the identification of functional sequence elements within it, such as protein coding genes and structural RNAs. Relative to protein coding genes, structural RNAs are more difficult to identify because of their reduced alphabet size, lack of open reading frames, and short length. Infernal is a software package that implements “covariance models” (CMs) for RNA homology search, which harness both sequence and structural conservation when searching for RNA homologs. Thanks to the added statistical signal inherent in the secondary structure conservation of many RNA families, Infernal is more powerful than sequence-only based methods such as BLAST and profile HMMs. Together with the Rfam database of CMs, Infernal is a useful tool for identifying RNAs in metagenomics data sets.
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Silverman IM, Li F, Gregory BD. Genomic era analyses of RNA secondary structure and RNA-binding proteins reveal their significance to post-transcriptional regulation in plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2013; 205-206:55-62. [PMID: 23498863 PMCID: PMC4079699 DOI: 10.1016/j.plantsci.2013.01.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2012] [Revised: 01/22/2013] [Accepted: 01/23/2013] [Indexed: 05/27/2023]
Abstract
The eukaryotic transcriptome is regulated both transcriptionally and post-transcriptionally. Transcriptional control was the major focus of early research efforts, while more recently post-transcriptional mechanisms have gained recognition for their significant regulatory importance. At the heart of post-transcriptional regulatory pathways are cis- and trans-acting features and factors including RNA secondary structure as well as RNA-binding proteins and their recognition sites on target RNAs. Recent advances in genomic methodologies have significantly improved our understanding of both RNA secondary structure and RNA-binding proteins and their regulatory effects within the eukaryotic transcriptome. In this review, we focus specifically on the collection of these regulatory moieties in plant transcriptomes. We describe the approaches for studying RNA secondary structure and RNA-protein interaction sites, with an emphasis on recent methodological advances that produce transcriptome-wide datasets. We discuss how these methods that include genome-wide RNA secondary structure determination and RNA-protein interaction site mapping are significantly improving our understanding of the functions of these two elements in post-transcriptional regulation. Finally, we delineate the need for additional genome-wide studies of RNA secondary structure and RNA-protein interactions in plants.
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Affiliation(s)
- Ian M. Silverman
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- PENN Genome Frontiers Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
- Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Fan Li
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- PENN Genome Frontiers Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
- Genomics and Computational Biology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Brian D. Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- PENN Genome Frontiers Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
- Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
- Genomics and Computational Biology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
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22
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Garcia-Martin JA, Clote P, Dotu I. RNAiFOLD: a constraint programming algorithm for RNA inverse folding and molecular design. J Bioinform Comput Biol 2013; 11:1350001. [PMID: 23600819 DOI: 10.1142/s0219720013500017] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Synthetic biology is a rapidly emerging discipline with long-term ramifications that range from single-molecule detection within cells to the creation of synthetic genomes and novel life forms. Truly phenomenal results have been obtained by pioneering groups--for instance, the combinatorial synthesis of genetic networks, genome synthesis using BioBricks, and hybridization chain reaction (HCR), in which stable DNA monomers assemble only upon exposure to a target DNA fragment, biomolecular self-assembly pathways, etc. Such work strongly suggests that nanotechnology and synthetic biology together seem poised to constitute the most transformative development of the 21st century. In this paper, we present a Constraint Programming (CP) approach to solve the RNA inverse folding problem. Given a target RNA secondary structure, we determine an RNA sequence which folds into the target structure; i.e. whose minimum free energy structure is the target structure. Our approach represents a step forward in RNA design--we produce the first complete RNA inverse folding approach which allows for the specification of a wide range of design constraints. We also introduce a Large Neighborhood Search approach which allows us to tackle larger instances at the cost of losing completeness, while retaining the advantages of meeting design constraints (motif, GC-content, etc.). Results demonstrate that our software, RNAiFold, performs as well or better than all state-of-the-art approaches; nevertheless, our approach is unique in terms of completeness, flexibility, and the support of various design constraints. The algorithms presented in this paper are publicly available via the interactive webserver http://bioinformatics.bc.edu/clotelab/RNAiFold; additionally, the source code can be downloaded from that site.
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Lacroix-Labonté J, Girard N, Lemieux S, Legault P. Helix-length compensation studies reveal the adaptability of the VS ribozyme architecture. Nucleic Acids Res 2011; 40:2284-93. [PMID: 22086962 PMCID: PMC3299992 DOI: 10.1093/nar/gkr1018] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Compensatory mutations in RNA are generally regarded as those that maintain base pairing, and their identification forms the basis of phylogenetic predictions of RNA secondary structure. However, other types of compensatory mutations can provide higher-order structural and evolutionary information. Here, we present a helix-length compensation study for investigating structure–function relationships in RNA. The approach is demonstrated for stem-loop I and stem-loop V of the Neurospora VS ribozyme, which form a kissing–loop interaction important for substrate recognition. To rapidly characterize the substrate specificity (kcat/KM) of several substrate/ribozyme pairs, a procedure was established for simultaneous kinetic characterization of multiple substrates. Several active substrate/ribozyme pairs were identified, indicating the presence of limited substrate promiscuity for stem Ib variants and helix-length compensation between stems Ib and V. 3D models of the I/V interaction were generated that are compatible with the kinetic data. These models further illustrate the adaptability of the VS ribozyme architecture for substrate cleavage and provide global structural information on the I/V kissing–loop interaction. By exploring higher-order compensatory mutations in RNA our approach brings a deeper understanding of the adaptability of RNA structure, while opening new avenues for RNA research.
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Affiliation(s)
- Julie Lacroix-Labonté
- Département de Biochimie, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, QC, Canada
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Bajaj P, Steger G, Hammann C. Sequence elements outside the catalytic core of natural hairpin ribozymes modulate the reactions differentially. Biol Chem 2011; 392:593-600. [PMID: 21657980 DOI: 10.1515/bc.2011.071] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract Hairpin ribozymes occur naturally only in the satellite RNAs of tobacco ringspot virus (TRsV), chicory yellow mottle virus (CYMoV) and arabis mosaic virus (ArMV). The catalytic centre of the predominantly studied sTRsV hairpin ribozyme, and of sArMV is organised around a four-way helical junction. We show here that sCYMoV features a five-way helical junction instead. Mutational analysis indicates that the fifth stem does not influence kinetic parameters of the sCYMoV hairpin ribozyme in vitro reactions, and therefore seems an appendix to that junction in the other ribozymes. We report further that all three ribozymes feature a three-way helical junction outside the catalytic core in stem A, with Watson-Crick complementarity to loop nucleotides in stem B. Kinetic analyses of cleavage and ligation reactions of several variants of the sTRsV and sCYMoV hairpin ribozymes in vitro show that the presence of this junction interferes with their reactions, particularly the ligation. We provide evidence that this is not due to a presumed interaction of the afore-mentioned elements in stems A and B. The evolutionary survival of this cis-inhibiting element seems rather to be caused by the coincidence of its position with that of the hammerhead ribozyme in the other RNA polarity.
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Affiliation(s)
- Preeti Bajaj
- Heisenberg Research Group Ribogenetics, Technical University of Darmstadt, Germany
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Seehafer C, Kalweit A, Steger G, Gräf S, Hammann C. From alpaca to zebrafish: hammerhead ribozymes wherever you look. RNA (NEW YORK, N.Y.) 2011; 17:21-6. [PMID: 21081661 PMCID: PMC3004062 DOI: 10.1261/rna.2429911] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The hammerhead ribozyme was originally discovered in subviral plant pathogens and was subsequently also found in a few other genomic locations. Using a secondary structure-based descriptor, we have searched publicly accessible sequence databases for new examples of type III hammerhead ribozymes. The more than 60,000 entries fulfilling the descriptor were filtered with respect to folding and stability parameters that were experimentally validated. This resulted in a set of 284 unique motifs, of which 124 represent database entries of known hammerhead ribozymes from subviral plant pathogens and A. thaliana. The remainder are 160 novel ribozyme candidates in 50 different eukaryotic genomes. With a few exceptions, the ribozymes were found either in repetitive DNA sequences or in introns of protein coding genes. Our data, which is complementary to a study by De la Peña and García-Robles in 2010, indicate that the hammerhead is the most abundant small endonucleolytic ribozyme, which, in view of no sequence conservation beyond the essential nucleotides, likely has evolved independently in different organisms.
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Grojean J, Downes B. Riboswitches as hormone receptors: hypothetical cytokinin-binding riboswitches in Arabidopsis thaliana. Biol Direct 2010; 5:60. [PMID: 20961447 PMCID: PMC2974657 DOI: 10.1186/1745-6150-5-60] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Accepted: 10/20/2010] [Indexed: 12/24/2022] Open
Abstract
Background Riboswitches are mRNA elements that change conformation when bound to small molecules. They are known to be key regulators of biosynthetic pathways in both prokaryotes and eukaryotes. Presentation of the Hypothesis The hypothesis presented here is that riboswitches function as receptors in hormone perception. We propose that riboswitches initiate or integrate signaling cascades upon binding to classic signaling molecules. The molecular interactions for ligand binding and gene expression control would be the same as for biosynthetic pathways, but the context and the cadre of ligands to consider is dramatically different. The hypothesis arose from the observation that a compound used to identify adenine binding RNA sequences is chemically similar to the classic plant hormone, or growth regulator, cytokinin. A general tenet of the hypothesis is that riboswitch-binding metabolites can be used to make predictions about chemically related signaling molecules. In fact, all cell permeable signaling compounds can be considered as potential riboswitch ligands. The hypothesis is plausible, as demonstrated by a cursory review of the transcriptome and genome of the model plant Arabidopsis thaliana for transcripts that i) contain an adenine aptamer motif, and ii) are also predicted to be cytokinin-regulated. Here, one gene, CRK10 (for Cysteine-rich Receptor-like Kinase 10, At4g23180), contains an adenine aptamer-related sequence and is down-regulated by cytokinin approximately three-fold in public gene expression data. To illustrate the hypothesis, implications of cytokinin-binding to the CRK10 mRNA are discussed. Testing the hypothesis At the broadest level, screening various cell permeable signaling molecules against random RNA libraries and comparing hits to sequence and gene expression data bases could determine how broadly the hypothesis applies. Specific cases, such as CRK10 presented here, will require experimental validation of direct ligand binding, altered RNA conformation, and effect on gene expression. Each case will be different depending on the signaling pathway and the physiology involved. Implications of the hypothesis This would be a very direct signal perception mechanism for regulating gene expression; rivaling animal steroid hormone receptors, which are frequently ligand dependent transcription initiation factors. Riboswitch-regulated responses could occur by modulating target RNA stability, translatability, and alternative splicing - all known expression platforms used in riboswitches. The specific illustration presented, CRK10, implies a new mechanism for the perception of cytokinin, a classic plant hormone. Experimental support for the hypothesis would add breadth to the growing list of important functions attributed to riboswitches. Reviewers This article was reviewed by Anthony Poole, Rob Knight, Mikhail Gelfand.
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Affiliation(s)
- Jeremy Grojean
- Saint Louis University, Department of Biology, 226 Macelwane Hall, St. Louis, MO 63103, USA
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28
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Current concepts in the treatment of retinitis pigmentosa. J Ophthalmol 2010; 2011:753547. [PMID: 21048997 PMCID: PMC2964907 DOI: 10.1155/2011/753547] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2010] [Accepted: 09/16/2010] [Indexed: 12/11/2022] Open
Abstract
Inherited retinal degenerations, including retinitis pigmentosa (RP) and Leber congenital amaurosis (LCA), affect 1 in 4000 individuals in the general population. A majority of the genes which are mutated in these conditions are expressed in either photoreceptors or the retinal pigment epithelium (RPE). There is considerable variation in the clinical severity of these conditions; the most severe being autosomal recessive LCA, a heterogeneous retinal degenerative disease and the commonest cause of congenital blindness in children. Here, we discuss all the potential treatments that are now available for retinal degeneration. A number of therapeutic avenues are being explored based on our knowledge of the pathophysiology of retinal degeneration derived from research on animal models, including: gene therapy, antiapoptosis agents, neurotrophic factors, and dietary supplementation. Technological advances in retinal implant devices continue to provide the promise of vision for patients with end-stage disease.
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de la Peña M, García-Robles I. Ubiquitous presence of the hammerhead ribozyme motif along the tree of life. RNA (NEW YORK, N.Y.) 2010; 16:1943-50. [PMID: 20705646 PMCID: PMC2941103 DOI: 10.1261/rna.2130310] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Examples of small self-cleaving RNAs embedded in noncoding regions already have been found to be involved in the control of gene expression, although their origin remains uncertain. In this work, we show the widespread occurrence of the hammerhead ribozyme (HHR) motif among genomes from the Bacteria, Chromalveolata, Plantae, and Metazoa kingdoms. Intergenic HHRs were detected in three different bacterial genomes, whereas metagenomic data from Galapagos Islands showed the occurrence of similar ribozymes that could be regarded as direct relics from the RNA world. Among eukaryotes, HHRs were detected in the genomes of three water molds as well as 20 plant species, ranging from unicellular algae to vascular plants. These HHRs were very similar to those previously described in small RNA plant pathogens and, in some cases, appeared as close tandem repetitions. A parallel situation of tandemly repeated HHR motifs was also detected in the genomes of lower metazoans from cnidarians to invertebrates, with special emphasis among hematophagous and parasitic organisms. Altogether, these findings unveil the HHR as a widespread motif in DNA genomes, which would be involved in new forms of retrotransposable elements.
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Affiliation(s)
- Marcos de la Peña
- Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), Valencia, Spain.
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30
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Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity. Nat Rev Genet 2009; 11:9-16. [PMID: 19935729 DOI: 10.1038/nrg2695] [Citation(s) in RCA: 301] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Transcriptome-wide studies in eukaryotes have been instrumental in the characterization of fundamental regulatory mechanisms for more than a decade. By contrast, in prokaryotes (bacteria and archaea) whole-transcriptome studies have not been performed until recently owing to the general view that microbial gene structures are simple, as well as technical difficulties in enriching for mRNAs that lack poly(A) tails. Deep RNA sequencing and tiling array studies are now revolutionizing our understanding of the complexity, plasticity and regulation of microbial transcriptomes.
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31
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Forrest ARR, Abdelhamid RF, Carninci P. Annotating non-coding transcription using functional genomics strategies. BRIEFINGS IN FUNCTIONAL GENOMICS AND PROTEOMICS 2009; 8:437-43. [PMID: 19833699 DOI: 10.1093/bfgp/elp041] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Non-coding RNA (ncRNA) transcripts are RNA molecules that do not code for proteins, but elicit function by other mechanisms. The vast majority of RNA produced in a cell is non-coding ribosomal RNA, produced from relatively few loci, however more recently complementary DNA (cDNA) cloning, tag sequencing, and genome tiling array studies suggest that ncRNAs also account for the majority of RNA species produced by a cell. ncRNA based regulation has been referred to as a 'hidden layer' of signals or 'dark matter' that control gene expression in cellular processes by poorly described mechanisms. These terms have appeared as ncRNAs until recently have been ignored by expression profiling and cDNA annotation projects and their mode of action is diverse (e.g. influencing chromatin structure and epigenetics, translational silencing, transcriptional silencing). Here, we highlight recent functional genomics strategies toward identifying and assigning function to ncRNA transcription.
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Affiliation(s)
- Alistair R R Forrest
- Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa 230-0045 Japan
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Scott WG, Martick M, Chi YI. Structure and function of regulatory RNA elements: ribozymes that regulate gene expression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2009; 1789:634-41. [PMID: 19781673 DOI: 10.1016/j.bbagrm.2009.09.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2009] [Revised: 09/01/2009] [Accepted: 09/13/2009] [Indexed: 01/14/2023]
Abstract
Since their discovery in the 1980s, it has gradually become apparent that there are several functional classes of naturally occurring ribozymes. These include ribozymes that mediate RNA splicing (the Group I and Group II introns, and possibly the RNA components of the spliceosome), RNA processing ribozymes (RNase P, which cleaves precursor tRNAs and other structural RNA precursors), the peptidyl transferase center of the ribosome, and small, self-cleaving genomic ribozymes (including the hammerhead, hairpin, HDV and VS ribozymes). The most recently discovered functional class of ribozymes include those that are embedded in the untranslated regions of mature mRNAs that regulate the gene's translational expression. These include the prokaryotic glmS ribozyme, a bacterial riboswitch, and a variant of the hammerhead ribozyme, which has been found embedded in mammalian mRNAs. With the discovery of a mammalian riboswitch ribozyme, the question of how an embedded hammerhead ribozyme's switching mechanism works becomes a compelling question. Recent structural results suggest several possibilities.
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Affiliation(s)
- William G Scott
- Center for the Molecular Biology of RNA, Sinsheimer Laboratory, University of California at Santa Cruz, Santa Cruz, CA, USA.
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Brown JW, Birmingham A, Griffiths PE, Jossinet F, Kachouri-Lafond R, Knight R, Lang BF, Leontis N, Steger G, Stombaugh J, Westhof E. The RNA structure alignment ontology. RNA (NEW YORK, N.Y.) 2009; 15:1623-31. [PMID: 19622678 PMCID: PMC2743057 DOI: 10.1261/rna.1601409] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2009] [Accepted: 05/26/2009] [Indexed: 05/19/2023]
Abstract
Multiple sequence alignments are powerful tools for understanding the structures, functions, and evolutionary histories of linear biological macromolecules (DNA, RNA, and proteins), and for finding homologs in sequence databases. We address several ontological issues related to RNA sequence alignments that are informed by structure. Multiple sequence alignments are usually shown as two-dimensional (2D) matrices, with rows representing individual sequences, and columns identifying nucleotides from different sequences that correspond structurally, functionally, and/or evolutionarily. However, the requirement that sequences and structures correspond nucleotide-by-nucleotide is unrealistic and hinders representation of important biological relationships. High-throughput sequencing efforts are also rapidly making 2D alignments unmanageable because of vertical and horizontal expansion as more sequences are added. Solving the shortcomings of traditional RNA sequence alignments requires explicit annotation of the meaning of each relationship within the alignment. We introduce the notion of "correspondence," which is an equivalence relation between RNA elements in sets of sequences as the basis of an RNA alignment ontology. The purpose of this ontology is twofold: first, to enable the development of new representations of RNA data and of software tools that resolve the expansion problems with current RNA sequence alignments, and second, to facilitate the integration of sequence data with secondary and three-dimensional structural information, as well as other experimental information, to create simultaneously more accurate and more exploitable RNA alignments.
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Abstract
Despite its small size, the complex behavior of the hammerhead ribozyme keeps surprising us, even more than 20 years after its discovery. Here, we summarize recent developments in the field, in particular the discovery of the first split hammerhead ribozyme.
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Affiliation(s)
- Christian Hammann
- Research Group Molecular Interactions, Department of Genetics, FB 18 Naturwissenschaften, Heinrich-Plett-Str. 40, Universität Kassel, D-34132 Kassel, Germany.
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Vicens Q, Cech TR. A natural ribozyme with 3',5' RNA ligase activity. Nat Chem Biol 2009; 5:97-9. [PMID: 19125157 PMCID: PMC2897744 DOI: 10.1038/nchembio.136] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2008] [Accepted: 12/08/2008] [Indexed: 01/10/2023]
Abstract
Using electrophoresis, sequencing and enzymatic digestion, we show that the group I intron from the cyanobacterium Anabaena sp. PCC 7120 catalyzes phosphodiester bond formation using a triphosphate on the 5'-terminal nucleotide, much like protein polymerases and engineered ribozymes. In the process, this ribozyme forms a unique circular RNA that incorporates the exogenous guanosine cofactor added during self-splicing. This finding may have relevance to a prebiotic RNA world and to modern biology.
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Affiliation(s)
- Quentin Vicens
- Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Colorado, UCB 215, Boulder, Colorado 80309-0215, USA.
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36
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Abstract
Riboswitches are vital components of many genomes. Covariance model searches for the characteristic architectures of riboswitch aptamer domains can be used to predict new examples of these structured RNAs. Since riboswitches generally function as cis-regulatory elements, examining the genomic contexts of these hits is critical for evaluating their biological relevance. With these two sources of comparative support, it is possible to identify riboswitches accurately from sequence information alone. Annotating riboswitches on a genomic scale enables more precise functions to be assigned to the proteins that they regulate, better defines their conserved aptamer structures by identifying diverged variants, and provides insight into how the genetic regulation of fundamental metabolic processes varies among species.
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Vicens Q, Paukstelis PJ, Westhof E, Lambowitz AM, Cech TR. Toward predicting self-splicing and protein-facilitated splicing of group I introns. RNA (NEW YORK, N.Y.) 2008; 14:2013-2029. [PMID: 18768647 PMCID: PMC2553746 DOI: 10.1261/rna.1027208] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2008] [Accepted: 07/08/2008] [Indexed: 05/26/2023]
Abstract
In the current era of massive discoveries of noncoding RNAs within genomes, being able to infer a function from a nucleotide sequence is of paramount interest. Although studies of individual group I introns have identified self-splicing and nonself-splicing examples, there is no overall understanding of the prevalence of self-splicing or the factors that determine it among the >2300 group I introns sequenced to date. Here, the self-splicing activities of 12 group I introns from various organisms were assayed under six reaction conditions that had been shown previously to promote RNA catalysis for different RNAs. Besides revealing that assessing self-splicing under only one condition can be misleading, this survey emphasizes that in vitro self-splicing efficiency is correlated with the GC content of the intron (>35% GC was generally conductive to self-splicing), and with the ability of the introns to form particular tertiary interactions. Addition of the Neurospora crassa CYT-18 protein activated splicing of two nonself-splicing introns, but inhibited the second step of self-splicing for two others. Together, correlations between sequence, predicted structure and splicing begin to establish rules that should facilitate our ability to predict the self-splicing activity of any group I intron from its sequence.
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Affiliation(s)
- Quentin Vicens
- Howard Hughes Medical Institute, University of Colorado, Department of Chemistry and Biochemistry, Boulder, Colorado 80309-0215, USA.
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Beniaminov A, Westhof E, Krol A. Distinctive structures between chimpanzee and human in a brain noncoding RNA. RNA (NEW YORK, N.Y.) 2008; 14:1270-1275. [PMID: 18511501 PMCID: PMC2441984 DOI: 10.1261/rna.1054608] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2008] [Accepted: 04/10/2008] [Indexed: 05/26/2023]
Abstract
Human accelerated region 1 (HAR1) is a short DNA region identified recently to have evolved the most rapidly among highly constrained regions since the divergence from our common ancestor with chimpanzee. It is transcribed as part of a noncoding RNA specifically expressed in the developing human neocortex. Employing a panoply of enzymatic and chemical probes, our analysis of HAR1 RNA proposed a secondary structure model differing from that published. Most surprisingly, we discovered that the substitutions between the chimpanzee and human sequences led the human HAR1 RNA to adopt a cloverleaf-like structure instead of an extended and unstable hairpin in the chimpanzee sequence. Thus, the rapid evolutionary changes resulted in a profound rearrangement of HAR1 RNA structure. Altogether, our results provide a structural context for elucidating HAR1 RNA function.
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Herschlag D, Chu VB. Unwinding RNA's secrets: advances in the biology, physics, and modeling of complex RNAs. Curr Opin Struct Biol 2008; 18:305-14. [PMID: 18555681 PMCID: PMC2574980 DOI: 10.1016/j.sbi.2008.05.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2008] [Accepted: 05/07/2008] [Indexed: 01/06/2023]
Abstract
The rapid development of our understanding of the diverse biological roles fulfilled by non-coding RNA has motivated interest in the basic macromolecular behavior, structure, and function of RNA. We focus on two areas in the behavior of complex RNAs. First, we present advances in the understanding of how RNA folding is accomplished in vivo by presenting a mechanism for the action of DEAD-box proteins. Members of this family are intimately associated with almost all cellular processes involving RNA, mediating RNA structural rearrangements and chaperoning their folding. Next, we focus on advances in understanding, and characterizing the basic biophysical forces that govern the folding of complex RNAs. Ultimately we expect that a confluence and synergy between these approaches will lead to profound understanding of RNA and its biology.
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Affiliation(s)
- Daniel Herschlag
- Department of Biochemistry, Stanford University, B400, Beckman Center, Stanford, CA 94305,
| | - Vincent B. Chu
- Department of Applied Physics, Stanford University, GLAM, McCullough 318, 476 Lomita Mall, Stanford, CA 94305,
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Serganov A, Patel DJ. Ribozymes, riboswitches and beyond: regulation of gene expression without proteins. Nat Rev Genet 2007; 8:776-90. [PMID: 17846637 PMCID: PMC4689321 DOI: 10.1038/nrg2172] [Citation(s) in RCA: 300] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Although various functions of RNA are carried out in conjunction with proteins, some catalytic RNAs, or ribozymes, which contribute to a range of cellular processes, require little or no assistance from proteins. Furthermore, the discovery of metabolite-sensing riboswitches and other types of RNA sensors has revealed RNA-based mechanisms that cells use to regulate gene expression in response to internal and external changes. Structural studies have shown how these RNAs can carry out a range of functions. In addition, the contribution of ribozymes and riboswitches to gene expression is being revealed as far more widespread than was previously appreciated. These findings have implications for understanding how cellular functions might have evolved from RNA-based origins.
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Affiliation(s)
- Alexander Serganov
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA.
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