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Nyberg KG, Navales FG, Keles E, Nguyen JQ, Hertz LM, Carthew RW. Robust and heritable knockdown of gene expression using a self-cleaving ribozyme in Drosophila. Genetics 2024; 227:iyae067. [PMID: 38701221 PMCID: PMC11304983 DOI: 10.1093/genetics/iyae067] [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: 01/19/2024] [Revised: 04/11/2024] [Accepted: 04/20/2024] [Indexed: 05/05/2024] Open
Abstract
The current toolkit for genetic manipulation in the model animal Drosophila melanogaster is extensive and versatile but not without its limitations. Here, we report a powerful and heritable method to knockdown gene expression in D. melanogaster using the self-cleaving N79 hammerhead ribozyme, a modification of a naturally occurring ribozyme found in the parasite Schistosoma mansoni. A 111-bp ribozyme cassette, consisting of the N79 ribozyme surrounded by insulating spacer sequences, was inserted into 4 independent long noncoding RNA genes as well as the male-specific splice variant of doublesex using scarless CRISPR/Cas9-mediated genome editing. Ribozyme-induced RNA cleavage resulted in robust destruction of 3' fragments typically exceeding 90%. Single molecule RNA fluorescence in situ hybridization results suggest that cleavage and destruction can even occur for nascent transcribing RNAs. Knockdown was highly specific to the targeted RNA, with no adverse effects observed in neighboring genes or the other splice variants. To control for potential effects produced by the simple insertion of 111 nucleotides into genes, we tested multiple catalytically inactive ribozyme variants and found that a variant with scrambled N79 sequence best recapitulated natural RNA levels. Thus, self-cleaving ribozymes offer a novel approach for powerful gene knockdown in Drosophila, with potential applications for the study of noncoding RNAs, nuclear-localized RNAs, and specific splice variants of protein-coding genes.
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Affiliation(s)
- Kevin G Nyberg
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Fritz Gerald Navales
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Eren Keles
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Joseph Q Nguyen
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Laura M Hertz
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Richard W Carthew
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
- NSF-Simons National Institute for Theory and Mathematics in Biology, Evanston, IL 60208, USA
- NSF-Simons Center for Quantitative Biology, Evanston, IL 60208, USA
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2
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Poddar A, Satthiyasilan N, Wang PH, Chen C, Yi R, Chandru K, Jia TZ. Reactions Driven by Primitive Nonbiological Polyesters. Acc Chem Res 2024; 57:2048-2057. [PMID: 39013010 DOI: 10.1021/acs.accounts.4c00167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
ConspectusAll life on Earth is composed of cells, which are built from and run by biological reactions and structures. These reactions and structures are generally the result of action by cellular biomolecules, which are indispensable for the function and survival of all living organisms. Specifically, biological catalysis, namely by protein enzymes, but also by other biomolecules including nucleic acids, is an essential component of life. How the biomolecules themselves that perform biological catalysis came to exist in the first place is a major unanswered question that plagues researchers to this day, which is generally the focus of the origins of life (OoL) research field. Based on current knowledge, it is generally postulated that early Earth was full of a myriad of different chemicals, and that these chemicals reacted in specific ways that led to the emergence of biochemistry, cells, and later, life. In particular, a significant part of OoL research focuses on the synthesis, evolution, and function of biomolecules potentially present under early Earth conditions, as a way to understand their eventual transition into modern life. However, this narrative overlooks possibilities that other molecules contributed to the OoL, as while biomolecules that led to life were certainly present on early Earth, at the same time, other molecules that may not have strict, direct biological lineage were also widely and abundantly present. For example, hydroxy acids, although playing a role in metabolism or as parts of certain biological structures, are not generally considered to be as essential to modern biology as amino acids (a chemically similar monomer), and thus research in the OoL field tends to perhaps focus more on amino acids than hydroxy acids. However, their likely abundance on early Earth coupled with their ability to spontaneously condense into polymers (i.e., polyesters) make hydroxy acids, and their subsequent products, functions, and reactions, a reasonable target of investigation for prebiotic chemists. Whether "non-biological" hydroxy acids or polyesters can contribute to the emergence of life on early Earth is an inquiry that deserves attention within the OoL community, as this knowledge can also contribute to our understanding of the plausibility of extraterrestrial life that does not exactly use the biochemical set found in terrestrial organisms. While some demonstrations have been made with respect to compartment assembly, compartmentalization, and growth of primitive polyester-based systems, whether these "non-biological" polymers can contribute any catalytic function and/or drive primitive reactions is still an important step toward the development of early life. Here, we review research both from the OoL field as well as from industry and applied sciences regarding potential catalysis or reaction driven by "non-biological" polyesters in various forms: as linear polymers, as hyperbranched polyesters, and as membraneless microdroplets.
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Affiliation(s)
- Arunava Poddar
- Blue Marble Space Institute of Science, 600 First Ave, Floor 1, Seattle, Washington 98104, United States
- Research Centre for Experimental Marine Biology and Biotechnology (PiE-UPV/EHU), University of the Basque Country, Areatza Pasealekua, 48620 Plentzia Bizkaia, Basque Country, Spain
| | - Nirmell Satthiyasilan
- Space Science Center (ANGKASA), Institute of Climate Change, National University of Malaysia, Bandar Baru Bangi, Selangor 43600, Malaysia
| | - Po-Hsiang Wang
- Graduate Institute of Environmental Engineering, National Central University, No. 300, Zhongda Rd., Zhongli District, Taoyuan 32001, Taiwan (Republic of China)
- Department of Chemical and Materials Engineering, National Central University, No. 300, Zhongda Rd., Zhongli District, Taoyuan 32001, Taiwan (R.O.C.)
| | - Chen Chen
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Biofunctional Catalyst Research Team, RIKEN Center for Sustainable Resource Science (CSRS), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Ruiqin Yi
- State Key Laboratory of Isotope Geochemistry and Chinese Academy of Sciences Center for Excellence in Deep Earth Science, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Kuhan Chandru
- Space Science Center (ANGKASA), Institute of Climate Change, National University of Malaysia, Bandar Baru Bangi, Selangor 43600, Malaysia
- Polymer Research Center (PORCE), Faculty of Science and Technology, National University of Malaysia, Bandar Baru Bangi, Selangor 43600, Malaysia
| | - Tony Z Jia
- Blue Marble Space Institute of Science, 600 First Ave, Floor 1, Seattle, Washington 98104, United States
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
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3
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McKinley LN, Meyer MO, Sebastian A, Chang BK, Messina KJ, Albert I, Bevilacqua PC. Direct testing of natural twister ribozymes from over a thousand organisms reveals a broad tolerance for structural imperfections. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.11.603121. [PMID: 39026743 PMCID: PMC11257566 DOI: 10.1101/2024.07.11.603121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Twister ribozymes are an extensively studied class of nucleolytic RNAs. Thousands of natural twisters have been proposed using sequence homology and structural descriptors. Yet, most of these candidates have not been validated experimentally. To address this gap, we developed CHiTA (Cleavage High-Throughput Assay), a high-throughput pipeline utilizing massively parallel oligonucleotide synthesis and next-generation sequencing to test putative ribozymes en masse in a scarless fashion. As proof of principle, we applied CHiTA to a small set of known active and mutant ribozymes. We then used CHiTA to test two large sets of naturally occurring twister ribozymes: over 1, 600 previously reported putative twisters and ∼1, 000 new candidate twisters. The new candidates were identified computationally in ∼1, 000 organisms, representing a massive increase in the number of ribozyme-harboring organisms. Approximately 94% of the twisters we tested were active and cleaved site-specifically. Analysis of their structural features revealed that many substitutions and helical imperfections can be tolerated. We repeated our computational search with structural descriptors updated from this analysis, whereupon we identified and confirmed the first intrinsically active twister ribozyme in mammals. CHiTA broadly expands the number of active twister ribozymes found in nature and provides a powerful method for functional analyses of other RNAs. GRAPHICAL ABSTRACT
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Liu G, Jiang H, Chen D, Murchie AIH. Identification of Hammerhead-variant ribozyme sequences in SARS-CoV-2. Nucleic Acids Res 2024; 52:3262-3277. [PMID: 38296822 PMCID: PMC11014351 DOI: 10.1093/nar/gkae037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/06/2024] [Accepted: 01/11/2024] [Indexed: 02/02/2024] Open
Abstract
The SARS-CoV-2 RNA virus and variants, responsible for the COVID-19 pandemic has become endemic, raised a need for further understanding of the viral genome and biology. Despite vast research on SARS-CoV-2, no ribozymes have been found in the virus genome. Here we report the identification of 39 Hammerhead-variant ribozyme sequences (CoV-HHRz) in SARS-CoV-2. These sequences are highly conserved within SARS-CoV-2 variants but show large diversity among other coronaviruses. In vitro CoV-HHRz sequences possess the characteristics of typical ribozymes; cleavage is pH and ion dependent, although their activity is relatively low and Mn2+ is required for cleavage. The cleavage sites of four CoV-HHRz coincide with the breakpoint of expressed subgenomic RNA (sgRNAs) in SARS-CoV-2 transcriptome data suggesting in vivo activity. The CoV-HHRz are involved in processing sgRNAs for ORF7b, ORF 10 and ORF1ab nsp13 which are essential for viral packaging and life cycle.
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Affiliation(s)
- Getong Liu
- Shanghai Pudong Hospital, Fudan University Pudong Medical Center and Institutes of Biomedical Sciences, Shanghai Medical College, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai 200032, China
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Hengyi Jiang
- Shanghai Pudong Hospital, Fudan University Pudong Medical Center and Institutes of Biomedical Sciences, Shanghai Medical College, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai 200032, China
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Dongrong Chen
- Shanghai Pudong Hospital, Fudan University Pudong Medical Center and Institutes of Biomedical Sciences, Shanghai Medical College, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai 200032, China
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Alastair I H Murchie
- Shanghai Pudong Hospital, Fudan University Pudong Medical Center and Institutes of Biomedical Sciences, Shanghai Medical College, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai 200032, China
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
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5
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Osman EA, Rynes TP, Wang YL, Mruk K, McKeague M. Non-invasive single cell aptasensing in live cells and animals. Chem Sci 2024; 15:4770-4778. [PMID: 38550682 PMCID: PMC10967030 DOI: 10.1039/d3sc05735f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 02/18/2024] [Indexed: 04/04/2024] Open
Abstract
We report a genetically encoded aptamer biosensor platform for non-invasive measurement of drug distribution in cells and animals. We combined the high specificity of aptamer molecular recognition with the easy-to-detect properties of fluorescent proteins. We generated six encoded aptasensors, showcasing the platform versatility. The biosensors display high sensitivity and specificity for detecting their specific drug target over related analogs. We show dose dependent response of biosensor performance reaching saturating drug uptake levels in individual live cells. We designed our platform for integration into animal genomes; thus, we incorporated aptamer biosensors into zebrafish, an important model vertebrate. The biosensors enabled non-invasive drug biodistribution imaging in whole animals across different timepoints. To our knowledge, this is the first example of an aptamer biosensor-expressing transgenic vertebrate that is carried through generations. As such, our encoded platform addresses the need for non-invasive whole animal biosensing ideal for pharmacokinetic-pharmacodynamic analyses that can be expanded to other organisms and to detect diverse molecules of interest.
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Affiliation(s)
- Eiman A Osman
- Department of Chemistry, Faculty of Science, McGill University Montreal QC H3A 0B8 Canada
| | - Thomas P Rynes
- Department of Pharmacology and Toxicology, Brody School of Medicine, East Carolina University Greenville NC 27834 USA
| | - Y Lucia Wang
- Pharmacology and Therapeutics, Faculty of Medicine and Health Sciences, McGill University Montreal QC H3G 1Y6 Canada
| | - Karen Mruk
- Department of Pharmacology and Toxicology, Brody School of Medicine, East Carolina University Greenville NC 27834 USA
| | - Maureen McKeague
- Department of Chemistry, Faculty of Science, McGill University Montreal QC H3A 0B8 Canada
- Pharmacology and Therapeutics, Faculty of Medicine and Health Sciences, McGill University Montreal QC H3G 1Y6 Canada
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6
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Kläge D, Müller E, Hartig JS. A comparative survey of the influence of small self-cleaving ribozymes on gene expression in human cell culture. RNA Biol 2024; 21:1-11. [PMID: 38146121 PMCID: PMC10761166 DOI: 10.1080/15476286.2023.2296203] [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] [Accepted: 12/13/2023] [Indexed: 12/27/2023] Open
Abstract
Self-cleaving ribozymes are versatile tools for synthetic biologists when it comes to controlling gene expression. Up to date, 12 different classes are known, and over the past decades more and more details about their structure, cleavage mechanisms and natural environments have been uncovered. However, when these motifs are applied to mammalian gene expression constructs, the outcome can often be unexpected. A variety of factors, such as surrounding sequences and positioning of the ribozyme influences the activity and hence performance of catalytic RNAs. While some information about the efficiency of individual ribozymes (each tested in specific contexts) is known, general trends obtained from standardized, comparable experiments are lacking, complicating decisions such as which ribozyme to choose and where to insert it into the target mRNA. In many cases, application-specific optimization is required, which can be very laborious. Here, we systematically compared different classes of ribozymes within the 3'-UTR of a given reporter gene. We then examined position-dependent effects of the best-performing ribozymes. Moreover, we tested additional variants of already widely used hammerhead ribozymes originating from various organisms. We were able to identify functional structures suited for aptazyme design and generated highly efficient hammerhead ribozyme variants originating from the human genome. The present dataset will aide decisions about how to apply ribozymes for affecting gene expression as well as for developing ribozyme-based switches for controlling gene expression in human cells.
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Affiliation(s)
- Dennis Kläge
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Konstanz, Germany
| | - Elisabeth Müller
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Konstanz, Germany
| | - Jörg S. Hartig
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Konstanz, Germany
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7
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Marotta NJ, Weinert EE. Insights into the metabolism, signaling, and physiological effects of 2',3'-cyclic nucleotide monophosphates in bacteria. Crit Rev Biochem Mol Biol 2023; 58:118-131. [PMID: 38064689 PMCID: PMC10877235 DOI: 10.1080/10409238.2023.2290473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 11/20/2023] [Indexed: 02/03/2024]
Abstract
2',3'-cyclic nucleotide monophosphates (2',3'-cNMPs) have been discovered within both prokaryotes and eukaryotes in the past decade and a half, raising questions about their conserved existence in cells. In plants and mammals, wounding has been found to cause increased levels of 2',3'-cNMPs. Roles for 2',3'-cNMPs in plant immunity suggest that their regulation may be valuable for both plant hosts and microbial pathogens. In support of this hypothesis, a plethora of microbial enzymes have been found with activities related to these molecules. Studies in bacteria suggest that 2',3'-cNMPs are also produced in response to cellular stress and modulate expression of numerous genes. 2',3'-cNMP levels affect bacterial phenotypes, including biofilm formation, motility, and growth. Within E. coli and Salmonella enterica, 2',3'-cNMPs are produced by RNA degradation by RNase I, highlighting potential roles for Type 2 RNases producing 2',3'-cNMPs in a range of organisms. Development of cellular tools to modulate 2',3'-cNMP levels in bacteria has allowed for interrogation of the effects of 2',3'-cNMP concentration on bacterial transcriptomes and physiology. Pull-downs of cellular 2',3'-cNMP binding proteins have identified the ribosome and in vitro studies demonstrated that 2',3'-cNMPs decrease translation, suggesting a direct mechanism for 2',3-cNMP-dependent control of bacterial phenotypes. Future studies dissecting the cellular roles of 2',3'-cNMPs will highlight novel signaling pathways within prokaryotes and which can potentially be engineered to control bacterial physiology.
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Affiliation(s)
- Nick J. Marotta
- Graduate Program in Molecular, Cellular, and Integrative
Biosciences, Penn State University, University Park, PA, 16803, USA
| | - Emily E. Weinert
- Department of Biochemistry and Molecular Biology, Penn
State University, University Park, PA, 16803, USA
- Department of Chemistry, Penn State University, University
Park, PA, 16803, USA
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8
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Najeh S, Zandi K, Kharma N, Perreault J. Computational design and experimental verification of pseudoknotted ribozymes. RNA (NEW YORK, N.Y.) 2023; 29:764-776. [PMID: 36868786 PMCID: PMC10187678 DOI: 10.1261/rna.079148.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 05/27/2022] [Indexed: 05/18/2023]
Abstract
The design of new RNA sequences that retain the function of a model RNA structure is a challenge in bioinformatics because of the structural complexity of these molecules. RNA can fold into its secondary and tertiary structures by forming stem-loops and pseudoknots. A pseudoknot is a set of base pairs between a region within a stem-loop and nucleotides outside of this stem-loop; this motif is very important for numerous functional structures. It is important for any computational design algorithm to take into account these interactions to give a reliable result for any structures that include pseudoknots. In our study, we experimentally validated synthetic ribozymes designed by Enzymer, which implements algorithms allowing for the design of pseudoknots. Enzymer is a program that uses an inverse folding approach to design pseudoknotted RNAs; we used it in this study to design two types of ribozymes. The ribozymes tested were the hammerhead and the glmS, which have a self-cleaving activity that allows them to liberate the new RNA genome copy during rolling-circle replication or to control the expression of the downstream genes, respectively. We demonstrated the efficiency of Enzymer by showing that the pseudoknotted hammerhead and glmS ribozymes sequences it designed were extensively modified compared to wild-type sequences and were still active.
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Affiliation(s)
- Sabrine Najeh
- INRS - Institut Armand-Frappier, Laval, QC H7V 1B7, Canada
| | - Kasra Zandi
- Software Engineering and Computer Science Department, Concordia University, Montreal, Quebec H3G 1M8, Canada
| | - Nawwaf Kharma
- Electrical and Computer Engineering Department, Concordia University, Montreal, Quebec H3G 1M8, Canada
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9
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Kelvin D, Suess B. Tapping the potential of synthetic riboswitches: reviewing the versatility of the tetracycline aptamer. RNA Biol 2023; 20:457-468. [PMID: 37459466 DOI: 10.1080/15476286.2023.2234732] [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] [Revised: 06/22/2023] [Accepted: 06/23/2023] [Indexed: 07/20/2023] Open
Abstract
Synthetic riboswitches are a versatile class of regulatory elements that are becoming increasingly established in synthetic biology applications. They are characterized by their compact size and independence from auxiliary protein factors. While naturally occurring riboswitches were mostly discovered in bacteria, synthetic riboswitches have been designed for all domains of life. Published design strategies far exceed the number of riboswitches found in nature. A core element of any riboswitch is a binding domain, called an aptamer, which is characterized by high specificity and affinity for its ligand. Aptamers can be selected de novo, allowing the design of synthetic riboswitches against a broad spectrum of targets. The tetracycline aptamer has proven to be well suited for riboswitch engineering. Since its selection, it has been used in a variety of applications and is considered to be well established and characterized. Using the tetracycline aptamer as an example, we aim to discuss a large variety of design approaches for synthetic riboswitch engineering and their application. We aim to demonstrate the versatility of riboswitches in general and the high potential of synthetic RNA devices for creating new solutions in both the scientific and medical fields.
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Affiliation(s)
- Daniel Kelvin
- Fachbereich Biologie, TU Darmstadt, Darmstadt, Germany
| | - Beatrix Suess
- Fachbereich Biologie, TU Darmstadt, Darmstadt, Germany
- Centre for Synthetic Biology, TU Darmstadt, Darmstadt, Germany
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10
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Stabilized Double-Stranded RNA Strategy Improves Cotton Resistance to CBW ( Anthonomus grandis). Int J Mol Sci 2022; 23:ijms232213713. [PMID: 36430188 PMCID: PMC9691246 DOI: 10.3390/ijms232213713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 11/11/2022] Open
Abstract
Cotton is the most important crop for fiber production worldwide. However, the cotton boll weevil (CBW) is an insect pest that causes significant economic losses in infested areas. Current control methods are costly, inefficient, and environmentally hazardous. Herein, we generated transgenic cotton lines expressing double-stranded RNA (dsRNA) molecules to trigger RNA interference-mediated gene silencing in CBW. Thus, we targeted three essential genes coding for chitin synthase 2, vitellogenin, and ecdysis-triggering hormone receptor. The stability of expressed dsRNAs was improved by designing a structured RNA based on a viroid genome architecture. We transformed cotton embryos by inserting a promoter-driven expression cassette that overexpressed the dsRNA into flower buds. The transgenic cotton plants were characterized, and positive PCR transformed events were detected with an average heritability of 80%. Expression of dsRNAs was confirmed in floral buds by RT-qPCR, and the T1 cotton plant generation was challenged with fertilized CBW females. After 30 days, data showed high mortality (around 70%) in oviposited yolks. In adult insects fed on transgenic lines, chitin synthase II and vitellogenin showed reduced expression in larvae and adults, respectively. Developmental delays and abnormalities were also observed in these individuals. Our data remark on the potential of transgenic cotton based on a viroid-structured dsRNA to control CBW.
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Rolling Circles as a Means of Encoding Genes in the RNA World. Life (Basel) 2022; 12:life12091373. [PMID: 36143408 PMCID: PMC9505818 DOI: 10.3390/life12091373] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/17/2022] [Accepted: 08/23/2022] [Indexed: 11/25/2022] Open
Abstract
The rolling circle mechanism found in viroids and some RNA viruses is a likely way that replication could have begun in the RNA World. Here, we consider simulations of populations of protocells, each containing multiple copies of rolling circle RNAs that can replicate non-enzymatically. The mechanism requires the presence of short self-cleaving ribozymes such as hammerheads, which can cleave and re-circularize RNA strands. A rolling circle must encode a hammerhead and the complement of a hammerhead, so that both plus and minus strands can cleave. Thus, the minimal functional length is twice the length of the hammerhead sequence. Selection for speed of replication will tend to reduce circles to this minimum length. However, if sequence errors occur when copying the hammerhead sequence, this prevents cleavage at one point, but still allows cleavage on the next passage around the rolling circle. Thus, there is a natural doubling mechanism that creates strands that are multiple times the length of the minimal sequence. This can provide space for the origin of new genes with beneficial functions. We show that if a beneficial gene appears in this new space, the longer sequence with the beneficial function can be selected, even though it replicates more slowly. This provides a route for the evolution of longer circles encoding multiple genes.
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12
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de la Peña M, Gago-Zachert S. A life of research on circular RNAs and ribozymes: towards the origin of viroids, deltaviruses and life. Virus Res 2022; 314:198757. [PMID: 35346751 DOI: 10.1016/j.virusres.2022.198757] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/14/2022] [Accepted: 03/24/2022] [Indexed: 12/31/2022]
Abstract
The first examples of circular RNAs (circRNAs) were reported in the '70s as a family of minimal infectious agents of flowering plants; the viroids and viral satellites of circRNA. In some cases, these small circular genomes encode self-cleaving RNA motifs or ribozymes, including an exceptional circRNA infecting not plants but humans: the Hepatitis Delta Virus. Autocatalytic ribozymes not only allowed to propose a common rolling-circle replication mechanism for all these subviral agents, but also a tentative link with the origin of life as molecular fossils of the so-called RNA world. Despite the weak biologic connection between angiosperm plants and the human liver, diverse scientists, and most notably Ricardo Flores, firmly supported an evolutionary relationship between plant viroids and human deltavirus agents. The tireless and inspiring work done by Ricardo's lab in the field of infectious circRNAs fuelled multiple hypotheses for the origin of these entities, allowing advances in other fields, from eukaryotic circRNAs to small ribozymes in genomes from all life kingdoms. The recent discovery of a plethora of viral-like circRNAs with ribozymes in disparate biological samples may finally allow us to connect plant and animal subviral agents, confirming again that Ricardo's eye for science was always a keen eye.
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Affiliation(s)
- Marcos de la Peña
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV). C/ Ingeniero Fausto Elio s/n, 46022, Valencia, Spain.
| | - Selma Gago-Zachert
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Section Microbial Biotechnology, Halle/Saale D-06120, Germany
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13
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In Memoriam of Ricardo Flores: The Career, Achievements, and Legacy of an inspirational plant virologist. Virus Res 2022. [DOI: 10.1016/j.virusres.2022.198718] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Kapadia JB, Kharma N, Davis AN, Kamel N, Perreault J. Toehold-mediated strand displacement to measure released product from self-cleaving ribozymes. RNA (NEW YORK, N.Y.) 2022; 28:263-273. [PMID: 34862273 PMCID: PMC8906547 DOI: 10.1261/rna.078823.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 10/27/2021] [Indexed: 06/13/2023]
Abstract
This paper presents a probe comprising a fluorophore and a quencher, enabling measurement of released product from self-cleaving hammerhead ribozyme, without labeled RNA molecules, regular sampling or use of polyacrylamide gels. The probe is made of two DNA strands; one strand is labeled with a fluorophore at its 5'-end, while the other strand is labeled with a quencher at its 3'-end. These two DNA strands are perfectly complementary, but with a 3'-overhang of the fluorophore strand. These unpaired nucleotides act as a toehold, which is utilized by a detached cleaved fragment (coming from a self-cleaving hammerhead ribozyme) as the starting point for a strand displacement reaction. This reaction causes the separation of the fluorophore strand from the quencher strand, culminating in fluorescence, detectable in a plate reader. Notably, the emitted fluorescence is proportional to the amount of detached cleaved-off RNAs, displacing the DNA quencher strand. This method can replace or complement radio-hazardous unstable 32P as a method of measurement of the product release from ribozyme cleavage reactions; it also eliminates the need for polyacrylamide gels, for the same purpose. Critically, this method allows to distinguish between the total amount of cleaved ribozymes and the amount of detached fragments, resulting from that cleavage reaction.
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Affiliation(s)
- Jay Bhakti Kapadia
- Electrical and Computer Engineering Department, Concordia University, Montreal, Quebec, Canada H3G 1M8
- INRS-Centre Armand-Frappier Santé Biotechnologie, Laval, Quebec, Canada H7V 1B7
| | - Nawwaf Kharma
- Electrical and Computer Engineering Department, Concordia University, Montreal, Quebec, Canada H3G 1M8
- Centre for Applied Synthetic Biology (CASB), Concordia University, Montreal, Quebec, Canada H4B 1R6
| | - Alen Nellikulam Davis
- Electrical and Computer Engineering Department, Concordia University, Montreal, Quebec, Canada H3G 1M8
| | - Nicolas Kamel
- Electrical and Computer Engineering Department, Concordia University, Montreal, Quebec, Canada H3G 1M8
| | - Jonathan Perreault
- INRS-Centre Armand-Frappier Santé Biotechnologie, Laval, Quebec, Canada H7V 1B7
- Centre for Applied Synthetic Biology (CASB), Concordia University, Montreal, Quebec, Canada H4B 1R6
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15
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Flores R, Navarro B, Serra P, Di Serio F. A scenario for the emergence of protoviroids in the RNA world and for their further evolution into viroids and viroid-like RNAs by modular recombinations and mutations. Virus Evol 2022; 8:veab107. [PMID: 35223083 PMCID: PMC8865084 DOI: 10.1093/ve/veab107] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 12/10/2021] [Accepted: 01/14/2022] [Indexed: 11/14/2022] Open
Abstract
Viroids are tiny, circular, and noncoding RNAs that are able to replicate and systemically infect plants. The smallest known pathogens, viroids have been proposed to represent survivors from the RNA world that likely preceded the cellular world currently dominating life on the earth. Although the small, circular, and compact nature of viroid genomes, some of which are also endowed with catalytic activity mediated by hammerhead ribozymes, support this proposal, the lack of feasible evolutionary routes and the identification of hammerhead ribozymes in a large number of DNA genomes of organisms along the tree of life have led some to question such a proposal. Here, we reassess the origin and subsequent evolution of viroids by complementing phylogenetic reconstructions with molecular data, including the primary and higher-order structure of the genomic RNAs, their replication, and recombination mechanisms and selected biological information. Features of some viroid-like RNAs found in plants, animals, and possibly fungi are also considered. The resulting evolutionary scenario supports the emergence of protoviroids in the RNA world, mainly as replicative modules, followed by a further increase in genome complexity based on module/domain shuffling and combination and mutation. Such a modular evolutionary scenario would have facilitated the inclusion in the protoviroid genomes of complex RNA structures (or coding sequences, as in the case of hepatitis delta virus and delta-like agents), likely needed for their adaptation from the RNA world to a life based on cells, thus generating the ancestors of current infectious viroids and viroid-like RNAs. Other noninfectious viroid-like RNAs, such as retroviroid-like RNA elements and retrozymes, could also be derived from protoviroids if their reverse transcription and integration into viral or eukaryotic DNA, respectively, are considered as a possible key step in their evolution. Comparison of evidence supporting a general and modular evolutionary model for viroids and viroid-like RNAs with that favoring alternative scenarios provides reasonable reasons to keep alive the hypothesis that these small RNA pathogens may be relics of a precellular world.
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Affiliation(s)
- Ricardo Flores
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas–Universidad Politécnica de Valencia, Ingeniero Fausto Elio s/n, Valencia 46022, Spain
| | - Beatriz Navarro
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Via Amendola 122/D, Bari 70126, Italy
| | - Pedro Serra
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas–Universidad Politécnica de Valencia, Ingeniero Fausto Elio s/n, Valencia 46022, Spain
| | - Francesco Di Serio
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Via Amendola 122/D, Bari 70126, Italy
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16
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Abstract
Informational macromolecules in biology are composed of subunits of a single handedness, d-nucleotides in nucleic acids and l-amino acids in proteins. Although this chiral uniformity may be expedient, it is not a chemical necessity, as demonstrated by the recent example of an RNA enzyme that catalyzes the RNA-templated polymerization of RNA molecules of the opposite handedness. This reaction, when carried out iteratively, can provide the basis for exponential amplification of RNA molecules and the information they contain. By carrying out thermal cycling, analogous to the polymerase chain reaction, and supplying oligonucleotide building blocks that comprise both the functional strand of RNA and its complement, cross-chiral exponential amplification was achieved. This process was used to amplify the l-RNA form of the hammerhead ribozyme, catalyzed by the d-RNA form of the polymerase. The resulting l-hammerhead exhibits the expected activity in cleaving a corresponding l-RNA substrate. Exponential amplification was also carried out within individual droplets of a water-in-oil emulsion. The ability to amplify enantio-RNAs, both in bulk solution and within compartments, provides a means to evolve cross-chiral RNA polymerases based on the function of the RNAs they produce.
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Affiliation(s)
- Grant A L Bare
- The Salk Institute, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Gerald F Joyce
- The Salk Institute, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
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17
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Stitz M, Chaparro C, Lu Z, Olzog VJ, Weinberg CE, Blom J, Goesmann A, Grunau C, Grevelding CG. Satellite-Like W-Elements: Repetitive, Transcribed, and Putative Mobile Genetic Factors with Potential Roles for Biology and Evolution of Schistosoma mansoni. Genome Biol Evol 2021; 13:6361599. [PMID: 34469545 PMCID: PMC8490949 DOI: 10.1093/gbe/evab204] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2021] [Indexed: 12/17/2022] Open
Abstract
A large portion of animal and plant genomes consists of noncoding DNA. This part includes tandemly repeated sequences and gained attention because it offers exciting insights into genome biology. We investigated satellite-DNA elements of the platyhelminth Schistosoma mansoni, a parasite with remarkable biological features. Schistosoma mansoni lives in the vasculature of humans causing schistosomiasis, a disease of worldwide importance. Schistosomes are the only trematodes that have evolved separate sexes, and the sexual maturation of the female depends on constant pairing with the male. The schistosome karyotype comprises eight chromosome pairs, males are homogametic (ZZ) and females are heterogametic (ZW). Part of the repetitive DNA of S. mansoni are W-elements (WEs), originally discovered as female-specific satellite DNAs in the heterochromatic block of the W-chromosome. Based on new genome and transcriptome data, we performed a reanalysis of the W-element families (WEFs). Besides a new classification of 19 WEFs, we provide first evidence for stage-, sex-, pairing-, gonad-, and strain-specific/preferential transcription of WEs as well as their mobile nature, deduced from autosomal copies of full-length and partial WEs. Structural analyses suggested roles as sources of noncoding RNA-like hammerhead ribozymes, for which we obtained functional evidence. Finally, the variable WEF occurrence in different schistosome species revealed remarkable divergence. From these results, we propose that WEs potentially exert enduring influence on the biology of S. mansoni. Their variable occurrence in different strains, isolates, and species suggests that schistosome WEs may represent genetic factors taking effect on variability and evolution of the family Schistosomatidae.
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Affiliation(s)
- Maria Stitz
- Institute of Parasitology, BFS, Justus Liebig University Giessen, Giessen, Germany
| | - Cristian Chaparro
- IHPE, CNRS, IFREMER, UPVD, University Montpellier, Perpignan, France
| | - Zhigang Lu
- Institute of Parasitology, BFS, Justus Liebig University Giessen, Giessen, Germany
| | | | | | - Jochen Blom
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Germany
| | - Christoph Grunau
- IHPE, CNRS, IFREMER, UPVD, University Montpellier, Perpignan, France
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18
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Mustafina K, Nomura Y, Rotrattanadumrong R, Yokobayashi Y. Circularly-Permuted Pistol Ribozyme: A Synthetic Ribozyme Scaffold for Mammalian Riboswitches. ACS Synth Biol 2021; 10:2040-2048. [PMID: 34374523 DOI: 10.1021/acssynbio.1c00213] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A small molecule-responsive self-cleaving ribozyme (aptazyme) embedded in the untranslated region of an mRNA functions as a riboswitch that allows chemical regulation of gene expression in mammalian cells. Aptazymes are engineered by fusing a self-cleaving ribozyme with an RNA aptamer that recognizes a small molecule so that the ribozyme is either activated or inhibited in the presence of the small molecule. However, the variety of aptamers, ribozymes, and aptazyme design strategies suitable for mammalian riboswitch applications is still limited. This work focuses on a new ribozyme scaffold for engineering aptazymes and riboswitches that function in mammalian cells. We investigated circularly permuted variants of the pistol ribozyme class (CPP) as a synthetic ribozyme scaffold for mammalian riboswitch applications. Through semirational design and high-throughput screening, we designed guanine and tetracycline activated riboswitches based on three distinct aptazyme architectures, resulting in riboswitches with ON/OFF ratios as high as 8.6. Our work adds CPP to the limited ribozyme scaffold toolbox for mammalian synthetic biology applications and highlights the opportunities in exploring ribozymes beyond natural motifs.
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Affiliation(s)
- Kamila Mustafina
- Nucleic Acid Chemistry and Engineering Unit Okinawa Institute of Science and Technology Graduate University Onna, Okinawa 904 0495, Japan
| | - Yoko Nomura
- Nucleic Acid Chemistry and Engineering Unit Okinawa Institute of Science and Technology Graduate University Onna, Okinawa 904 0495, Japan
| | - Rachapun Rotrattanadumrong
- Nucleic Acid Chemistry and Engineering Unit Okinawa Institute of Science and Technology Graduate University Onna, Okinawa 904 0495, Japan
| | - Yohei Yokobayashi
- Nucleic Acid Chemistry and Engineering Unit Okinawa Institute of Science and Technology Graduate University Onna, Okinawa 904 0495, Japan
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19
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Rolling-circle and strand-displacement mechanisms for non-enzymatic RNA replication at the time of the origin of life. J Theor Biol 2021; 527:110822. [PMID: 34214567 DOI: 10.1016/j.jtbi.2021.110822] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 06/11/2021] [Accepted: 06/26/2021] [Indexed: 11/21/2022]
Abstract
It is likely that RNA replication began non-enzymatically, and that polymerases were later selected to speed up the process. We consider replication mechanisms in modern viruses and ask which of these is possible non-enzymatically, using mathematical models and experimental data found in the literature to estimate rates of RNA synthesis and replication. Replication via alternating plus and minus strands is found in some single-stranded RNA viruses. However, if this occurred non-enzymatically it would lead to double-stranded RNA that would not separate. With some form of environmental cycling, such as temperature, salinity, or pH cycling, double-stranded RNA can be melted to form single-stranded RNA, although re-annealing of existing strands would then occur much faster than synthesis of new strands. We show that re-annealing blocks this form of replication at a very low concentration of strands. Other kinds of viruses synthesize linear double strands from single strands and then make new single strands from double strands via strand-displacement. This does not require environmental cycling and is not blocked by re-annealing. However, under non-enzymatic conditions, if strand-displacement occurs from a linear template, we expect the incomplete new strand to be almost always displaced by the tail end of the old strand through toehold-mediated displacement. A third kind of replication in viruses and viroids is rolling-circle replication which occurs via strand-displacement on a circular template. Rolling-circle replication does not require environmental cycling and is not prevented by toehold-mediated displacement. Rolling-circle replication is therefore expected to occur non-enzymatically and is a likely starting point for the evolution of polymerase-catalysed replication.
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20
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Schmidt CM, Smolke CD. A convolutional neural network for the prediction and forward design of ribozyme-based gene-control elements. eLife 2021; 10:59697. [PMID: 33860764 PMCID: PMC8128436 DOI: 10.7554/elife.59697] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 04/15/2021] [Indexed: 12/12/2022] Open
Abstract
Ribozyme switches are a class of RNA-encoded genetic switch that support conditional regulation of gene expression across diverse organisms. An improved elucidation of the relationships between sequence, structure, and activity can improve our capacity for de novo rational design of ribozyme switches. Here, we generated data on the activity of hundreds of thousands of ribozyme sequences. Using automated structural analysis and machine learning, we leveraged these large data sets to develop predictive models that estimate the in vivo gene-regulatory activity of a ribozyme sequence. These models supported the de novo design of ribozyme libraries with low mean basal gene-regulatory activities and new ribozyme switches that exhibit changes in gene-regulatory activity in the presence of a target ligand, producing functional switches for four out of five aptamers. Our work examines how biases in the model and the data set that affect prediction accuracy can arise and demonstrates that machine learning can be applied to RNA sequences to predict gene-regulatory activity, providing the basis for design tools for functional RNAs.
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Affiliation(s)
- Calvin M Schmidt
- Department of Bioengineering, Stanford University, Stanford, United States
| | - Christina D Smolke
- Department of Bioengineering, Stanford University, Stanford, United States.,Chan Zuckerberg Biohub, San Francisco, United States
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21
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Panchapakesan SSS, Breaker RR. The case of the missing allosteric ribozymes. Nat Chem Biol 2021; 17:375-382. [PMID: 33495645 PMCID: PMC8880209 DOI: 10.1038/s41589-020-00713-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 11/13/2020] [Indexed: 01/28/2023]
Abstract
The RNA World theory encompasses the hypothesis that sophisticated ribozymes and riboswitches were the primary drivers of metabolic processes in ancient organisms. Several types of catalytic RNAs and many classes of ligand-sensing RNA switches still exist in modern cells. Curiously, allosteric ribozymes formed by the merger of RNA enzyme and RNA switch components are largely absent in today's biological systems. This is true despite the striking abundances of various classes of both self-cleaving ribozymes and riboswitch aptamers. Here we present the known types of ligand-controlled ribozymes and riboswitches and discuss the possible reasons why fused ribozyme-aptamer constructs have been disfavored through evolution.
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Affiliation(s)
- Shanker S. S. Panchapakesan
- Department of Molecular, Cellular and Developmental
Biology, Yale University, P.O. Box 208103, New Haven, CT 06520-8103, USA
| | - Ronald R. Breaker
- Department of Molecular, Cellular and Developmental
Biology, Yale University, P.O. Box 208103, New Haven, CT 06520-8103, USA.,Howard Hughes Medical Institute, Yale University, P.O. Box
208103, New Haven, CT 06520-8103, USA.,Department of Molecular Biophysics and Biochemistry, Yale
University, P.O. Box 208103, New Haven, CT 06520-8103, USA
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22
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Goguen RP, Gatignol A, Scarborough RJ. Cloning and Detection of Aptamer-Ribozyme Conjugations. Methods Mol Biol 2021; 2167:253-267. [PMID: 32712924 DOI: 10.1007/978-1-0716-0716-9_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
RNA aptamers can be used to target proteins or nucleic acids for therapeutic purposes and are candidates for RNA-mediated gene therapy. Like other small therapeutic RNAs, they can be expressed in cells from DNA templates that include a cellular promoter upstream of the RNA coding sequence. Secondary structures flanking aptamers can be used to enhance the activity or stability of these molecules. Notably, flanking self-cleaving ribozymes to remove extraneous nucleotides included during transcription as well as flanking hairpins to improve RNA stability have been used to increase the effect of therapeutic aptamers. Here we describe the cloning procedure of aptamers containing different flanking secondary structures and methods to compare their expression levels by a northern blot protocol optimized for the detection of small RNA molecules.
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Affiliation(s)
- Ryan P Goguen
- Lady Davis Institute for Medical Research, Montréal, QC, Canada.,Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada
| | - Anne Gatignol
- Lady Davis Institute for Medical Research, Montréal, QC, Canada. .,Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada. .,Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC, Canada.
| | - Robert J Scarborough
- Lady Davis Institute for Medical Research, Montréal, QC, Canada. .,Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada.
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23
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Moelling K, Broecker F. Viroids and the Origin of Life. Int J Mol Sci 2021; 22:ijms22073476. [PMID: 33800543 PMCID: PMC8036462 DOI: 10.3390/ijms22073476] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 03/24/2021] [Accepted: 03/24/2021] [Indexed: 11/16/2022] Open
Abstract
Viroids are non-coding circular RNA molecules with rod-like or branched structures. They are often ribozymes, characterized by catalytic RNA. They can perform many basic functions of life and may have played a role in evolution since the beginning of life on Earth. They can cleave, join, replicate, and undergo Darwinian evolution. Furthermore, ribozymes are the essential elements for protein synthesis of cellular organisms as parts of ribosomes. Thus, they must have preceded DNA and proteins during evolution. Here, we discuss the current evidence for viroids or viroid-like RNAs as a likely origin of life on Earth. As such, they may also be considered as models for life on other planets or moons in the solar system as well as on exoplanets.
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Affiliation(s)
- Karin Moelling
- Institute of Medical Microbiology, University of Zurich, Gloriastr 30, 8006 Zurich, Switzerland
- Max Planck Institute for molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
- Correspondence: ; Tel.: +49-(172)-3274306
| | - Felix Broecker
- Vaxxilon Deutschland GmbH, Magnusstr. 11, 12489 Berlin, Germany;
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24
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Dönmüş B, Ünal S, Kirmizitaş FC, Türkoğlu Laçin N. Virus-associated ribozymes and nano carriers against COVID-19. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2021; 49:204-218. [PMID: 33645342 DOI: 10.1080/21691401.2021.1890103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a zoo tonic, highly pathogenic virus. The new type of coronavirus with contagious nature spread from Wuhan (China) to the whole world in a very short time and caused the new coronavirus disease (COVID-19). COVID-19 has turned into a global public health crisis due to spreading by close person-to-person contact with high transmission capacity. Thus, research about the treatment of the damages caused by the virus or prevention from infection increases everyday. Besides, there is still no approved and definitive, standardized treatment for COVID-19. However, this disaster experienced by human beings has made us realize the significance of having a system ready for use to prevent humanity from viral attacks without wasting time. As is known, nanocarriers can be targeted to the desired cells in vitro and in vivo. The nano-carrier system targeting a specific protein, containing the enzyme inhibiting the action of the virus can be developed. The system can be used by simple modifications when we encounter another virus epidemic in the future. In this review, we present a potential treatment method consisting of a nanoparticle-ribozyme conjugate, targeting ACE-2 receptors by reviewing the virus-associated ribozymes, their structures, types and working mechanisms.
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Affiliation(s)
- Beyza Dönmüş
- Molecular Biology and Genetics Department, Yıldız Technical University, Istanbul, Turkey
| | - Sinan Ünal
- Molecular Biology and Genetics Department, Yıldız Technical University, Istanbul, Turkey
| | - Fatma Ceren Kirmizitaş
- Molecular Biology and Genetics Department, Yıldız Technical University, Istanbul, Turkey
| | - Nelisa Türkoğlu Laçin
- Molecular Biology and Genetics Department, Yıldız Technical University, Istanbul, Turkey
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25
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Cervera A, de la Peña M. Cloning and Detection of Genomic Retrozymes and Their circRNA Intermediates. Methods Mol Biol 2021; 2167:27-44. [PMID: 32712913 DOI: 10.1007/978-1-0716-0716-9_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Retrozymes are a novel family of non-autonomous retrotransposable elements that contain hammerhead ribozyme motifs. These retroelements are found widespread in eukaryotic genomes, with active copies present in many species, which rely on other autonomous transposons for mobilization. Contrary to other retrotransposons, transcription of retrozymes in vivo leads to the formation and accumulation of circular RNAs, which can be readily detected by RNA blotting. In this chapter, we describe the procedures needed to carry out the cloning of genomic retrozymes, and to detect by northern blot their circular RNA retrotransposition intermediates.
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Affiliation(s)
- Amelia Cervera
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València (CSIS-UPV), Valencia, Spain
| | - Marcos de la Peña
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València (CSIS-UPV), Valencia, Spain.
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26
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Abstract
Self-cleaving ribozymes are RNA molecules that catalyze a site-specific self-scission reaction. Analysis of self-cleavage is a crucial aspect of the biochemical study and understanding of these molecules. Here we describe a co-transcriptional assay that allows the analysis of self-cleaving ribozymes in different reaction conditions and in the presence of desired ligands and/or cofactors. Utilizing a standard T7 RNA polymerase in vitro transcription system under limiting Mg2+ concentration, followed by a 25-fold dilution of the reaction in desired conditions of self-cleavage (buffer, ions, ligands, pH, temperature, etc.) to halt the synthesis of new RNA molecules, allows the study of self-scission of these molecules without the need for purification or additional preparation steps, such as refolding procedures. Furthermore, because the transcripts are not denatured, this assay likely yields RNAs in conformations relevant to co-transcriptionally folded species in vivo.
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27
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A Singular and Widespread Group of Mobile Genetic Elements: RNA Circles with Autocatalytic Ribozymes. Cells 2020; 9:cells9122555. [PMID: 33260527 PMCID: PMC7761336 DOI: 10.3390/cells9122555] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 11/19/2020] [Accepted: 11/26/2020] [Indexed: 11/16/2022] Open
Abstract
Circular DNAs, such as most prokaryotic and phage genomes, are a frequent form of nucleic acids, whereas circular RNAs had been regarded as unusual macromolecules until very recently. The first reported RNA circles were the family of small infectious genomes of viroids and circular RNA (circRNA) satellites of plant viruses, some of which contain small self-cleaving RNA motifs, such as the hammerhead (HHR) and hairpin ribozymes. A similar infectious circRNA, the unique human hepatitis delta virus (HDV), is another viral satellite that also encodes self-cleaving motifs called HDV ribozymes. Very recently, different animals have been reported to contain HDV-like circRNAs with typical HDV ribozymes, but also conserved HHR motifs, as we describe here. On the other hand, eukaryotic and prokaryotic genomes encode sequences able to self-excise as circRNAs, like the autocatalytic Group I and II introns, which are widespread genomic mobile elements. In the 1990s, the first circRNAs encoded in a mammalian genome were anecdotally reported, but their abundance and importance have not been unveiled until recently. These gene-encoded circRNAs are produced by events of alternative splicing in a process generally known as backsplicing. However, we have found a second natural pathway of circRNA expression conserved in numerous plant and animal genomes, which efficiently promotes the accumulation of small non-coding RNA circles through the participation of HHRs. Most of these genome-encoded circRNAs with HHRs are the transposition intermediates of a novel family of non-autonomous retrotransposons called retrozymes, with intriguing potential as new forms of gene regulation.
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28
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Khoshbin Z, Housaindokht MR, Izadyar M, Bozorgmehr MR, Verdian A. Recent advances in computational methods for biosensor design. Biotechnol Bioeng 2020; 118:555-578. [PMID: 33135778 DOI: 10.1002/bit.27618] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 09/25/2020] [Accepted: 10/29/2020] [Indexed: 01/20/2023]
Abstract
Biosensors are analytical tools with a great application in healthcare, food quality control, and environmental monitoring. They are of considerable interest to be designed by using cost-effective and efficient approaches. Designing biosensors with improved functionality or application in new target detection has been converted to a fast-growing field of biomedicine and biotechnology branches. Experimental efforts have led to valuable successes in the field of biosensor design; however, some deficiencies restrict their utilization for this purpose. Computational design of biosensors is introduced as a promising key to eliminate the gap. A set of reliable structure prediction of the biosensor segments, their stability, and accurate descriptors of molecular interactions are required to computationally design biosensors. In this review, we provide a comprehensive insight into the progress of computational methods to guide the design and development of biosensors, including molecular dynamics simulation, quantum mechanics calculations, molecular docking, virtual screening, and a combination of them as the hybrid methodologies. By relying on the recent advances in the computational methods, an opportunity emerged for them to be complementary or an alternative to the experimental methods in the field of biosensor design.
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Affiliation(s)
- Zahra Khoshbin
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | | | - Mohammad Izadyar
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | | | - Asma Verdian
- Department of Food Safety and Quality Control, Research Institute of Food Science and Technology (RIFST), Mashhad, Iran
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29
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Kruse RL, Legras X, Barzi M. Cre/LoxP-HBV plasmids generating recombinant covalently closed circular DNA genome upon transfection. Virus Res 2020; 292:198224. [PMID: 33166564 DOI: 10.1016/j.virusres.2020.198224] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/18/2020] [Accepted: 11/03/2020] [Indexed: 02/08/2023]
Abstract
New therapies against hepatitis B virus (HBV) require the elimination of covalently closed circular DNA (cccDNA), the episomal HBV genome. HBV plasmids containing an overlength 1.3-mer genome and bacterial backbone (pHBV1.3) are used in many different models, but do not replicate the unique features of cccDNA. Since the stable cccDNA pool is a barrier to HBV eradication in patients, we developed a recombinant circular HBV genome (rcccDNA) to mimic the cccDNA using Cre/LoxP technology. We validated four LoxP insertion sites into the HBV genome using hydrodynamic tail vein injection into murine liver, demonstrating high levels of HBV surface antigen (HBsAg) and HBV DNA expression with rcccDNA formation. HBsAg expression from rcccDNA was >30,000 ng/mL over 78 days, while HBsAg-expression from pHBV1.3 plasmid DNA declined from 2753 ng/mL to 131 ng/mL over that time in immunodeficient mice (P < 0.001), reflective of plasmid DNA silencing. We then cloned Cre-recombinase in cis on the LoxP-HBV plasmids, achieving plasmid stability in bacteria with intron insertion into Cre and demonstrating rcccDNA formation after transfection in vitro and in vivo. These cis-Cre/LoxP-HBV plasmids were then used to create HBx-mutant and GFP reporter plasmids to further probe cccDNA biology and antiviral strategies against cccDNA. Overall, we believe these auto-generating rcccDNA plasmids will be of great value to model cccDNA for testing new therapies against HBV infection.
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Affiliation(s)
- Robert L Kruse
- Center for Cell and Gene Therapy, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
| | - Xavier Legras
- Center for Cell and Gene Therapy, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Mercedes Barzi
- Center for Cell and Gene Therapy, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
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30
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Cervera A, de la Peña M. Small circRNAs with self-cleaving ribozymes are highly expressed in diverse metazoan transcriptomes. Nucleic Acids Res 2020; 48:5054-5064. [PMID: 32198887 PMCID: PMC7229834 DOI: 10.1093/nar/gkaa187] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 03/09/2020] [Accepted: 03/11/2020] [Indexed: 12/13/2022] Open
Abstract
Ribozymes are catalytic RNAs present in modern genomes but regarded as remnants of a prebiotic RNA world. The paradigmatic hammerhead ribozyme (HHR) is a small self-cleaving motif widespread from bacterial to human genomes. Here, we report that most of the classical type I HHRs frequently found in the genomes of animals are contained within a novel family of non-autonomous non-LTR retrotransposons of the retrozyme class. These retroelements are expressed as abundant linear and circular RNAs of ∼170-400 nt in different animal tissues. Bioinformatic and in vitro analyses indicate an efficient self-cleavage of the HHRs harboured in most invertebrate retrozymes, whereas HHRs in retrozymes of vertebrates, such as the axolotl and other amphibians, require to act as dimeric motifs to reach higher self-cleavage rates. Ligation assays of retrozyme RNAs with a protein ligase versus HHR self-ligation indicate that, most likely, tRNA ligases and not the ribozymes are involved in the step of RNA circularization. Altogether, these results confirm the existence of a new and conserved pathway in animals and, likely, eukaryotes in general, for the efficient biosynthesis of RNA circles through small ribozymes, which opens the door for the development of new tools in the emerging field of study of circRNAs.
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Affiliation(s)
- Amelia Cervera
- IBMCP (CSIC-UPV). C/ Ingeniero Fausto Elio s/n, 46022 Valencia, Spain
| | - Marcos de la Peña
- IBMCP (CSIC-UPV). C/ Ingeniero Fausto Elio s/n, 46022 Valencia, Spain
- To whom correspondence should be addressed. Tel: +34 963 877 915; Fax: +34 963 877 859;
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Abstract
The term “prion” was originally coined to describe the proteinaceous infectious agents involved in mammalian neurological disorders. More recently, a prion has been defined as a nonchromosomal, protein-based genetic element that is capable of converting the copies of its own benign variant into the prion form, with the new phenotypic effects that can be transmitted through the cytoplasm. Some prions are toxic to the cell, are able to aggregate and/or form amyloid structures, and may be infectious in the wild, but none of those traits are seen as an integral property of all prions. The term “prion” was originally coined to describe the proteinaceous infectious agents involved in mammalian neurological disorders. More recently, a prion has been defined as a nonchromosomal, protein-based genetic element that is capable of converting the copies of its own benign variant into the prion form, with the new phenotypic effects that can be transmitted through the cytoplasm. Some prions are toxic to the cell, are able to aggregate and/or form amyloid structures, and may be infectious in the wild, but none of those traits are seen as an integral property of all prions. We propose that the definition of prion should be expanded, to include the inducible transmissible entities undergoing autocatalytic conversion and consisting of RNA rather than protein. We show that when seen in this framework, some naturally occurring RNAs, including ribozymes, riboswitches, viroids, viroid-like retroelements, and PIWI-interacting RNAs (piRNAs), possess several of the characteristic properties of prions.
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32
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Footprints of a Singular 22-Nucleotide RNA Ring at the Origin of Life. BIOLOGY 2020; 9:biology9050088. [PMID: 32344921 PMCID: PMC7285048 DOI: 10.3390/biology9050088] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 04/06/2020] [Accepted: 04/19/2020] [Indexed: 11/17/2022]
Abstract
(1) Background: Previous experimental observations and theoretical hypotheses have been providing insight into a hypothetical world where an RNA hairpin or ring may have debuted as the primary informational and functional molecule. We propose a model revisiting the architecture of RNA-peptide interactions at the origin of life through the evolutionary dynamics of RNA populations. (2) Methods: By performing a step-by-step computation of the smallest possible hairpin/ring RNA sequences compatible with building up a variety of peptides of the primitive network, we inferred the sequence of a singular docosameric RNA molecule, we call the ALPHA sequence. Then, we searched for any relics of the peptides made from ALPHA in sequences deposited in the different public databases. (3) Results: Sequence matching between ALPHA and sequences from organisms among the earliest forms of life on Earth were found at high statistical relevance. We hypothesize that the frequency of appearance of relics from ALPHA sequence in present genomes has a functional necessity. (4) Conclusions: Given the fitness of ALPHA as a supportive sequence of the framework of all existing theories, and the evolution of Archaea and giant viruses, it is anticipated that the unique properties of this singular archetypal ALPHA sequence should prove useful as a model matrix for future applications, ranging from synthetic biology to DNA computing.
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33
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Novikov IB, Wilkins AD, Lichtarge O. An Evolutionary Trace method defines functionally important bases and sites common to RNA families. PLoS Comput Biol 2020; 16:e1007583. [PMID: 32208421 PMCID: PMC7092961 DOI: 10.1371/journal.pcbi.1007583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 11/27/2019] [Indexed: 11/18/2022] Open
Abstract
Functional non-coding (fnc)RNAs are nucleotide sequences of varied lengths, structures, and mechanisms that ubiquitously influence gene expression and translation, genome stability and dynamics, and human health and disease. Here, to shed light on their functional determinants, we seek to exploit the evolutionary record of variation and divergence read from sequence comparisons. The approach follows the phylogenetic Evolutionary Trace (ET) paradigm, first developed and extensively validated on proteins. We assigned a relative rank of importance to every base in a study of 1070 functional RNAs, including the ribosome, and observed evolutionary patterns strikingly similar to those seen in proteins, namely, (1) the top-ranked bases clustered in secondary and tertiary structures. (2) In turn, these clusters mapped functional regions for catalysis, binding proteins and drugs, post-transcriptional modification, and deleterious mutations. (3) Moreover, the quantitative quality of these clusters correlated with the identification of functional regions. (4) As a result of this correlation, smoother structural distributions of evolutionary important nucleotides improved functional site predictions. Thus, in practice, phylogenetic analysis can broadly identify functional determinants in RNA sequences and functional sites in RNA structures, and reveal details on the basis of RNA molecular functions. As example of application, we report several previously undocumented and potentially functional ET nucleotide clusters in the ribosome. This work is broadly relevant to studies of structure-function in ribonucleic acids. Additionally, this generalization of ET shows that evolutionary constraints among sequence, structure, and function are similar in structured RNA and proteins. RNA ET is currently available as part of the ET command-line package, and will be available as a web-server. Traditionally, RNA has been delegated to the role of an intermediate between DNA and proteins. However, we now recognize that RNAs are broadly functional beyond their role in translation, and that a number of diverse classes exist. Because functional, non-coding RNAs are prevalent in biology and impact human health, it is important to better understand their functional determinants. However, the classical solution to this problem, targeted mutagenesis, is time-consuming and scales poorly. We propose an alternative computational approach to this problem, the Evolutionary Trace method. Previously developed and validated for proteins, Evolutionary Trace examines evolutionary history of a molecule and predicts evolutionarily important residues in the sequence. We apply Evolutionary Trace to a set of diverse RNAs, and find that the evolutionarily important nucleotides cluster on the three-dimensional structure, and that these clusters closely overlap functional sites. We also find that the clustering property can be used to refine and improve predictions. These findings are in close agreement with our observations of Evolutionary Trace in proteins, and suggest that structured functional RNAs and proteins evolve under similar constraints. In practice, the approach is to be used by RNA researches seeking insight into their molecule of interest, and the Evolutionary Trace program, along with a working example, is available at https://github.com/LichtargeLab/RNA_ET_ms.
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Affiliation(s)
- Ilya B. Novikov
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Angela D. Wilkins
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail:
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34
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Naghdi MR, Boutet E, Mucha C, Ouellet J, Perreault J. Single Mutation in Hammerhead Ribozyme Favors Cleavage Activity with Manganese over Magnesium. Noncoding RNA 2020; 6:E14. [PMID: 32245091 PMCID: PMC7151607 DOI: 10.3390/ncrna6010014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/16/2020] [Accepted: 03/18/2020] [Indexed: 12/11/2022] Open
Abstract
Hammerhead ribozymes are one of the most studied classes of ribozymes so far, from both the structural and biochemical point of views. The activity of most hammerhead ribozymes is cation-dependent. Mg2+ is one of the most abundant divalent cations in the cell and therefore plays a major role in cleavage activity for most hammerhead ribozymes. Besides Mg2+, cleavage can also occur in the presence of other cations such as Mn2+. The catalytic core of hammerhead ribozymes is highly conserved, which could contribute to a preference of hammerhead ribozymes toward certain cations. Here, we show a naturally occurring variation in the catalytic core of hammerhead ribozymes, A6C, that can favor one metallic ion, Mn2+, over several other cations.
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Affiliation(s)
- Mohammad Reza Naghdi
- Institut National de la Recherche Scientifique (INRS), Centre Armand Frappier Santé Biotechnologie, 531 boul. des Prairies, Laval, QB H7V 1B7, Canada; (M.R.N.); (E.B.); (C.M.)
| | - Emilie Boutet
- Institut National de la Recherche Scientifique (INRS), Centre Armand Frappier Santé Biotechnologie, 531 boul. des Prairies, Laval, QB H7V 1B7, Canada; (M.R.N.); (E.B.); (C.M.)
| | - Clarisse Mucha
- Institut National de la Recherche Scientifique (INRS), Centre Armand Frappier Santé Biotechnologie, 531 boul. des Prairies, Laval, QB H7V 1B7, Canada; (M.R.N.); (E.B.); (C.M.)
| | - Jonathan Ouellet
- Department of Chemistry and Physics, Monmouth University, 400 Cedar Avenue, West Long Branch, NJ 07764, USA;
| | - Jonathan Perreault
- Institut National de la Recherche Scientifique (INRS), Centre Armand Frappier Santé Biotechnologie, 531 boul. des Prairies, Laval, QB H7V 1B7, Canada; (M.R.N.); (E.B.); (C.M.)
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35
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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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36
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Yamada M, Tanaka Y. Structure-activity relationship of pseudoknot-type hammerhead ribozyme reveals key structural elements for enhanced catalytic activity †. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2019; 39:245-257. [PMID: 31578927 DOI: 10.1080/15257770.2019.1669169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The pseudoknot-type hammerhead ribozyme (PK-HHRz) is known to be activated by a pseudoknot interaction between loops I and II. To obtain maximal activation through the pseudoknot formation, we studied the structure-activity relationship of PK-HHRz. From these studies, the structural requirements of the PK-HHRz cleavage reaction were clearly defined. In addition, we discovered a PK-HHRz with higher cleavage activity than the wild-type sequence. Although modifications generally disrupt the activity of enzymes, in this case the elongation of loop II increased the activity of PK-HHRz. These new findings will form a structural basis for designing PK-HHRz variants for gene-therapeutic/manipulating agents and biochemical/nanotechnological tools.
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Affiliation(s)
- Mituhiro Yamada
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan.,Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Yoshiyuki Tanaka
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan.,Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Tokushima, Japan
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37
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Gaines CS, Giese TJ, York DM. Cleaning Up Mechanistic Debris Generated by Twister Ribozymes Using Computational RNA Enzymology. ACS Catal 2019; 9:5803-5815. [PMID: 31328021 PMCID: PMC6641568 DOI: 10.1021/acscatal.9b01155] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The catalytic properties of RNA have been a subject of fascination and intense research since their discovery over 30 years ago. Very recently, several classes of nucleolytic ribozymes have emerged and been characterized structurally. Among these, the twister ribozyme has been center-stage, and a topic of debate about its architecture and mechanism owing to conflicting interpretations of different crystal structures, and in some cases conflicting interpretations of the same functional data. In the present work, we attempt to clean up the mechanistic "debris" generated by twister ribozymes using a comprehensive computational RNA enzymology approach aimed to provide a unified interpretation of existing structural and functional data. Simulations in the crystalline environment and in solution provide insight into the origins of observed differences in crystal structures, and coalesce on a common active site architecture, and dynamical ensemble in solution. We use GPU-accelerated free energy methods with enhanced sampling to ascertain microscopic nucleobase pK a values of the implicated general acid and base, from which predicted activity-pH profiles can be compared directly with experiments. Next, ab initio quantum mechanical/molecular mechanical (QM/MM) simulations with full dynamic solvation under periodic boundary conditions are used to determine mechanistic pathways through multi-dimensional free energy landscapes for the reaction. We then characterize the rate-controlling transition state, and make predictions about kinetic isotope effects and linear free energy relations. Computational mutagenesis is performed to explain the origin of rate effects caused by chemical modifications and make experimentally testable predictions. Finally, we provide evidence that helps to resolve conflicting issues related to the role of metal ions in catalysis. Throughout each stage, we highlight how a conserved L-platform structural motif, to- gether with a key L-anchor residue, forms the characteristic active site scaffold enabling each of the catalytic strategies to come together not only for the twister ribozyme, but the majority of the known small nucleolytic ribozyme classes.
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Affiliation(s)
- Colin S. Gaines
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Timothy J. Giese
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Darrin M. York
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
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38
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Demongeot J, Norris V. Emergence of a "Cyclosome" in a Primitive Network Capable of Building "Infinite" Proteins. Life (Basel) 2019; 9:E51. [PMID: 31216720 PMCID: PMC6617141 DOI: 10.3390/life9020051] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/08/2019] [Accepted: 06/13/2019] [Indexed: 01/02/2023] Open
Abstract
We argue for the existence of an RNA sequence, called the AL (for ALpha) sequence, which may have played a role at the origin of life; this role entailed the AL sequence helping generate the first peptide assemblies via a primitive network. These peptide assemblies included "infinite" proteins. The AL sequence was constructed on an economy principle as the smallest RNA ring having one representative of each codon's synonymy class and capable of adopting a non-functional but nevertheless evolutionarily stable hairpin form that resisted denaturation due to environmental changes in pH, hydration, temperature, etc. Long subsequences from the AL ring resemble sequences from tRNAs and 5S rRNAs of numerous species like the proteobacterium, Rhodobacter sphaeroides. Pentameric subsequences from the AL are present more frequently than expected in current genomes, in particular, in genes encoding some of the proteins associated with ribosomes like tRNA synthetases. Such relics may help explain the existence of universal sequences like exon/intron frontier regions, Shine-Dalgarno sequence (present in bacterial and archaeal mRNAs), CRISPR and mitochondrial loop sequences.
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Affiliation(s)
- Jacques Demongeot
- Faculty of Medicine, Université Grenoble Alpes, AGEIS EA 7407 Tools for e-Gnosis Medical, 38700 La Tronche, France.
| | - Vic Norris
- Laboratory of Microbiology Signals and Microenvironment, Université de Rouen, 76821 Mont-Saint-Aignan CEDEX, France.
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39
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Hepatitis E Virus Drug Development. Viruses 2019; 11:v11060485. [PMID: 31141919 PMCID: PMC6631701 DOI: 10.3390/v11060485] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 05/20/2019] [Accepted: 05/24/2019] [Indexed: 02/08/2023] Open
Abstract
Hepatitis E virus (HEV) is an underestimated disease, leading to estimated 20 million infections and up to 70,000 deaths annually. Infections are mostly asymptomatic but can reach mortality rates up to 25% in pregnant women or become chronic in immunocompromised patients. The current therapy options are limited to the unspecific antivirals Ribavirin (RBV) and pegylated Interferon-α (pegIFN-α). RBV leads to viral clearance in only 80% of patients treated, and is, similar to pegIFN-α, contraindicated in the major risk group of pregnant women, emphasizing the importance of new therapy options. In this review, we focus on the urgent need and current efforts in HEV drug development. We provide an overview of the current status of HEV antiviral research. Furthermore, we discuss strategies for drug development and the limitations of the approaches with respect to HEV.
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40
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Catalán P, Elena SF, Cuesta JA, Manrubia S. Parsimonious Scenario for the Emergence of Viroid-Like Replicons De Novo. Viruses 2019; 11:v11050425. [PMID: 31075860 PMCID: PMC6563258 DOI: 10.3390/v11050425] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 04/30/2019] [Accepted: 05/02/2019] [Indexed: 01/12/2023] Open
Abstract
Viroids are small, non-coding, circular RNA molecules that infect plants. Different hypotheses for their evolutionary origin have been put forward, such as an early emergence in a precellular RNA World or several de novo independent evolutionary origins in plants. Here, we discuss the plausibility of de novo emergence of viroid-like replicons by giving theoretical support to the likelihood of different steps along a parsimonious evolutionary pathway. While Avsunviroidae-like structures are relatively easy to obtain through evolution of a population of random RNA sequences of fixed length, rod-like structures typical of Pospiviroidae are difficult to fix. Using different quantitative approaches, we evaluated the likelihood that RNA sequences fold into a rod-like structure and bear specific sequence motifs facilitating interactions with other molecules, e.g., RNA polymerases, RNases, and ligases. By means of numerical simulations, we show that circular RNA replicons analogous to Pospiviroidae emerge if evolution is seeded with minimal circular RNAs that grow through the gradual addition of nucleotides. Further, these rod-like replicons often maintain their structure if independent functional modules are acquired that impose selective constraints. The evolutionary scenario we propose here is consistent with the structural and biochemical properties of viroids described to date.
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Affiliation(s)
- Pablo Catalán
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK.
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain.
| | - Santiago F Elena
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de València, Paterna, 46980 València, Spain.
- The Santa Fe Institute, Santa Fe, NM 87501, USA.
| | - José A Cuesta
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain.
- Departamento de Matemáticas, Universidad Carlos III de Madrid, 28911 Leganés, Spain.
- Instituto de Biocomputación y Física de Sistemas Complejos (BiFi), Universidad de Zaragoza, 50018 Zaragoza, Spain.
- Institute of Financial Big Data (IFiBiD), Universidad Carlos III de Madrid⁻Banco de Santander, 28903 Getafe, Spain.
| | - Susanna Manrubia
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain.
- National Biotechnology Centre (CSIC), 28049 Madrid, Spain.
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41
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Parmeciano Di Noto G, Molina MC, Quiroga C. Insights Into Non-coding RNAs as Novel Antimicrobial Drugs. Front Genet 2019; 10:57. [PMID: 30853970 PMCID: PMC6395445 DOI: 10.3389/fgene.2019.00057] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 01/24/2019] [Indexed: 12/21/2022] Open
Abstract
Multidrug resistant bacteria are a serious worldwide problem, especially carbapenem-resistant Enterobacteriaceae (such as Klebsiella pneumoniae and Escherichia coli), Acinetobacter baumannii and Pseudomonas aeruginosa. Since the emergence of extensive and pan-drug resistant bacteria there are few antibiotics left to treat patients, thus novel RNA-based strategies are being considered. Here, we examine the current situation of different non-coding RNAs found in bacteria as well as their function and potential application as antimicrobial agents. Furthermore, we discuss the factors that may contribute in the efficient development of RNA-based drugs, the limitations for their implementation and the use of nanocarriers for delivery.
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Affiliation(s)
- Gisela Parmeciano Di Noto
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPAM), Facultad de Medicina, Buenos Aires, Argentina
| | - María Carolina Molina
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPAM), Facultad de Medicina, Buenos Aires, Argentina
| | - Cecilia Quiroga
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPAM), Facultad de Medicina, Buenos Aires, Argentina
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42
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Nakano SI, Yamashita H, Tanabe K, Sugimoto N. Bulky cations greatly increase the turnover of a native hammerhead ribozyme. RSC Adv 2019; 9:35820-35824. [PMID: 35528091 PMCID: PMC9074697 DOI: 10.1039/c9ra06797c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 10/28/2019] [Indexed: 12/13/2022] Open
Abstract
Methods to facilitate the catalytic turnover of ribozymes are required for advancing oligonucleotide-based technologies. This study examined tetraalkylammonium ions for their ability to increase the efficiency of catalytic turnover of a native hammerhead ribozyme. Kinetic analysis showed that large tetraalkylammonium ions significantly increased the turnover rate of the ribozyme and was much more effective than poly(ethylene glycol) (PEG) and urea. The magnitude of the rate increase depended on the concentrations of Mg2+ and tetrapentylammonium ions, and the rate was enhanced by more than 180-fold at the optimal concentrations of these salts. The results provide physical insights into interactions of ribozymes with large cationic molecules through electrostatic forces and steric hindrance. Large tetraalkylammonium ions increase the turnover rate of the ribozyme derived from an intronic ribozyme in the human genome. The rate can be enhanced by more than a hundred-fold at the optimal concentrations of Mg2+ and TPeA ions.![]()
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Affiliation(s)
- Shu-ichi Nakano
- Department of Nanobiochemistry
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST)
- Konan University
- Kobe
- Japan
| | - Hirofumi Yamashita
- Department of Nanobiochemistry
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST)
- Konan University
- Kobe
- Japan
| | - Kazuya Tanabe
- Department of Nanobiochemistry
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST)
- Konan University
- Kobe
- Japan
| | - Naoki Sugimoto
- Department of Nanobiochemistry
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST)
- Konan University
- Kobe
- Japan
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43
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Reverse Genetics for Peste des Petits Ruminants Virus: Current Status and Lessons to Learn from Other Non-segmented Negative-Sense RNA Viruses. Virol Sin 2018; 33:472-483. [PMID: 30456658 PMCID: PMC6335227 DOI: 10.1007/s12250-018-0066-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 10/11/2018] [Indexed: 11/20/2022] Open
Abstract
Peste des petits ruminants (PPR) is a highly contagious transboundary animal disease with a severe socio-economic impact on the livestock industry, particularly in poor countries where it is endemic. Full understanding of PPR virus (PPRV) pathobiology and molecular biology is critical for effective control and eradication of the disease. To achieve these goals, establishment of stable reverse genetics systems for PPRV would play a key role. Unfortunately, this powerful technology remains less accessible and poorly documented for PPRV. In this review, we discussed the current status of PPRV reverse genetics as well as the recent innovations and advances in the reverse genetics of other non-segmented negative-sense RNA viruses that could be applicable to PPRV. These strategies may contribute to the improvement of existing techniques and/or the development of new reverse genetics systems for PPRV.
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Hayakawa Y, Banno A, Kitagawa H, Higashi S, Kitade Y, Shibata A, Ikeda M. Reduction-Responsive DNA Duplex Containing O 6-Nitrobenzyl-Guanine. ACS OMEGA 2018; 3:9267-9275. [PMID: 31459058 PMCID: PMC6645092 DOI: 10.1021/acsomega.8b01177] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/01/2018] [Indexed: 05/27/2023]
Abstract
Stimuli-controlled structural transitions of nucleic acids have received growing attentions owing to their potential applications in the fields of chemical and synthetic biology. Here, we describe the development of reduction-responsive deoxyribonucleic acid (DNA) duplexes, in which guanine rings bearing a reduction-responsive cleavable nitrobenzyl (NB) group at the O 6 position (GNB) are introduced at defined positions. We demonstrate that the artificial NB group can be removed in response to reduction stimulus without the dissociation of the intermolecular duplex structure, which comprises a G-quadruplex forming nucleic acid strand with one GNB and its complementary sequence with one mismatch pair. Meanwhile, another duplex that comprised a G-quadruplex forming nucleic acid strand with two GNB and its complementary sequence with three mismatch pairs exhibited reduction-responsive structural transitions from intermolecular duplex to intramolecular quadruplex. These findings might be useful for the development of DNA architectures endowed with reduction-responsive functions.
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Affiliation(s)
- Yukiko Hayakawa
- Department
of Life Science and Chemistry, Graduate School of Natural
Science and Technology and United Graduate School of Drug Discovery and Medical
Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Ayaka Banno
- Department
of Life Science and Chemistry, Graduate School of Natural
Science and Technology and United Graduate School of Drug Discovery and Medical
Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Hiroaki Kitagawa
- Department
of Life Science and Chemistry, Graduate School of Natural
Science and Technology and United Graduate School of Drug Discovery and Medical
Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Sayuri Higashi
- Department
of Life Science and Chemistry, Graduate School of Natural
Science and Technology and United Graduate School of Drug Discovery and Medical
Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Yukio Kitade
- Department
of Life Science and Chemistry, Graduate School of Natural
Science and Technology and United Graduate School of Drug Discovery and Medical
Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Aya Shibata
- Department
of Life Science and Chemistry, Graduate School of Natural
Science and Technology and United Graduate School of Drug Discovery and Medical
Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Masato Ikeda
- Department
of Life Science and Chemistry, Graduate School of Natural
Science and Technology and United Graduate School of Drug Discovery and Medical
Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
- Center
for Highly Advanced Integration of Nano and Life Sciences, Gifu University (G-CHAIN), Gifu 501-1193, Japan
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45
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Stroehlein AJ, Young ND, Korhonen PK, Hall RS, Jex AR, Webster BL, Rollinson D, Brindley PJ, Gasser RB. The small RNA complement of adult Schistosoma haematobium. PLoS Negl Trop Dis 2018; 12:e0006535. [PMID: 29813122 PMCID: PMC5993326 DOI: 10.1371/journal.pntd.0006535] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 06/08/2018] [Accepted: 05/17/2018] [Indexed: 01/24/2023] Open
Abstract
Background Blood flukes of the genus Schistosoma cause schistosomiasis—a neglected tropical disease (NTD) that affects more than 200 million people worldwide. Studies of schistosome genomes have improved our understanding of the molecular biology of flatworms, but most of them have focused largely on protein-coding genes. Small non-coding RNAs (sncRNAs) have been explored in selected schistosome species and are suggested to play essential roles in the post-transcriptional regulation of genes, and in modulating flatworm-host interactions. However, genome-wide small RNA data are currently lacking for key schistosomes including Schistosoma haematobium—the causative agent of urogenital schistosomiasis of humans. Methodology MicroRNAs (miRNAs) and other sncRNAs of male and female adults of S. haematobium and small RNA transcription levels were explored by deep sequencing, genome mapping and detailed bioinformatic analyses. Principal findings In total, 89 transcribed miRNAs were identified in S. haematobium—a similar complement to those reported for the congeners S. mansoni and S. japonicum. Of these miRNAs, 34 were novel, with no homologs in other schistosomes. Most miRNAs (n = 64) exhibited sex-biased transcription, suggestive of roles in sexual differentiation, pairing of adult worms and reproductive processes. Of the sncRNAs that were not miRNAs, some related to the spliceosome (n = 21), biogenesis of other RNAs (n = 3) or ribozyme functions (n = 16), whereas most others (n = 3798) were novel (‘orphans’) with unknown functions. Conclusions This study provides the first genome-wide sncRNA resource for S. haematobium, extending earlier studies of schistosomes. The present work should facilitate the future curation and experimental validation of sncRNA functions in schistosomes to enhance our understanding of post-transcriptional gene regulation and of the roles that sncRNAs play in schistosome reproduction, development and parasite-host cross-talk. Human schistosomiasis is a chronic, neglected tropical disease (NTD) that is predominantly caused by the blood flukes Schistosoma haematobium, S. mansoni and S. japonicum. Infections by S. haematobium and/or S. mansoni are highly prevalent in Africa, affecting ~ 200 million people. The decoding of schistosome draft genomes has, to some extent, improved our understanding of the molecular biology of these parasites and now allows for non-protein-coding regions in these genomes to be characterised. Here, we explored small RNAs in adult S. haematobium by deep sequencing, reference genome mapping and detailed bioinformatic analyses. This study provides the first genome-wide miRNA and sncRNA resource for S. haematobium, extending earlier work on schistosomes and facilitating future curation efforts and functional investigations of schistosome sncRNAs. These efforts should enable a better understanding of post-transcriptional RNA modifications, gene regulation and novel aspects of parasite development, parasite-host cross-talk and disease at the molecular level.
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Affiliation(s)
- Andreas J. Stroehlein
- Melbourne Veterinary School, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
- * E-mail: (AJS); (RBG)
| | - Neil D. Young
- Melbourne Veterinary School, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Pasi K. Korhonen
- Melbourne Veterinary School, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Ross S. Hall
- Melbourne Veterinary School, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Aaron R. Jex
- Melbourne Veterinary School, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
- Population Health and Immunity, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Bonnie L. Webster
- Parasites and Vectors Division, The Natural History Museum, London, United Kingdom
| | - David Rollinson
- Parasites and Vectors Division, The Natural History Museum, London, United Kingdom
| | - Paul J. Brindley
- School of Medicine & Health Sciences, Department of Microbiology, Immunology & Tropical Medicine, The George Washington University, Washington, DC, United States of America
| | - Robin B. Gasser
- Melbourne Veterinary School, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
- * E-mail: (AJS); (RBG)
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Šponer J, Bussi G, Krepl M, Banáš P, Bottaro S, Cunha RA, Gil-Ley A, Pinamonti G, Poblete S, Jurečka P, Walter NG, Otyepka M. RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview. Chem Rev 2018; 118:4177-4338. [PMID: 29297679 PMCID: PMC5920944 DOI: 10.1021/acs.chemrev.7b00427] [Citation(s) in RCA: 336] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Indexed: 12/14/2022]
Abstract
With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics. Computer simulations, and in particular atomistic molecular dynamics (MD), allow structural dynamics of biomolecular systems to be investigated with unprecedented temporal and spatial resolution. We here provide a comprehensive overview of the fast-developing field of MD simulations of RNA molecules. We begin with an in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods. We also survey the closely related field of coarse-grained modeling of RNA systems. After dealing with the methodological aspects, we provide an exhaustive overview of the available RNA simulation literature, ranging from studies of the smallest RNA oligonucleotides to investigations of the entire ribosome. Our review encompasses tetranucleotides, tetraloops, a number of small RNA motifs, A-helix RNA, kissing-loop complexes, the TAR RNA element, the decoding center and other important regions of the ribosome, as well as assorted others systems. Extended sections are devoted to RNA-ion interactions, ribozymes, riboswitches, and protein/RNA complexes. Our overview is written for as broad of an audience as possible, aiming to provide a much-needed interdisciplinary bridge between computation and experiment, together with a perspective on the future of the field.
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Affiliation(s)
- Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences , Kralovopolska 135 , Brno 612 65 , Czech Republic
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences , Kralovopolska 135 , Brno 612 65 , Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Sandro Bottaro
- Structural Biology and NMR Laboratory, Department of Biology , University of Copenhagen , Copenhagen 2200 , Denmark
| | - Richard A Cunha
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Alejandro Gil-Ley
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Giovanni Pinamonti
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Simón Poblete
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Petr Jurečka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Nils G Walter
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
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Abstract
The emergence of functional cooperation between the three main classes of biomolecules - nucleic acids, peptides and lipids - defines life at the molecular level. However, how such mutually interdependent molecular systems emerged from prebiotic chemistry remains a mystery. A key hypothesis, formulated by Crick, Orgel and Woese over 40 year ago, posits that early life must have been simpler. Specifically, it proposed that an early primordial biology lacked proteins and DNA but instead relied on RNA as the key biopolymer responsible not just for genetic information storage and propagation, but also for catalysis, i.e. metabolism. Indeed, there is compelling evidence for such an 'RNA world', notably in the structure of the ribosome as a likely molecular fossil from that time. Nevertheless, one might justifiably ask whether RNA alone would be up to the task. From a purely chemical perspective, RNA is a molecule of rather uniform composition with all four bases comprising organic heterocycles of similar size and comparable polarity and pK a values. Thus, RNA molecules cover a much narrower range of steric, electronic and physicochemical properties than, e.g. the 20 amino acid side-chains of proteins. Herein we will examine the functional potential of RNA (and other nucleic acids) with respect to self-replication, catalysis and assembly into simple protocellular entities.
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48
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Serra P, Messmer A, Sanderson D, James D, Flores R. Apple hammerhead viroid-like RNA is a bona fide viroid: Autonomous replication and structural features support its inclusion as a new member in the genus Pelamoviroid. Virus Res 2018; 249:8-15. [PMID: 29510173 DOI: 10.1016/j.virusres.2018.03.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 03/02/2018] [Accepted: 03/02/2018] [Indexed: 01/11/2023]
Abstract
Apple hammerhead viroid-like RNA (AHVd RNA) has been reported in different apple cultivars and geographic regions and, considering the presence of hammerhead ribozymes in both polarity strands, suspected to be either a viroid of the family Avsunviroidae or a viroid-like satellite RNA. Here we report that dimeric head-to-tail in vitro transcripts of a 433-nt reference variant of AHVd RNA from cultivar "Pacific Gala" are infectious when mechanically inoculated to apple, thus showing that this RNA is a bona fide viroid for which we have kept the name apple hammerhead viroid (AHVd) until its pathogenicity, if any, is better assessed. By combining thermodynamics-based predictions with co-variation analyses of the natural genetic diversity found in AHVd we have inferred the most likely conformations for both AHVd polarity strands in vivo, with that of the (+) polarity strand being stabilized by a kissing loop-interaction similar to those reported in peach latent mosaic viroid and chrysathemum chlorotic mottle viroid, the two known members of the genus Pelamoviroid (family Avsunviroidae). Therefore, AHVd RNA fulfills the biological and molecular criteria to be allocated to this genus, the members of which, intriguingly, display low global sequence identity but high structural conservation.
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Affiliation(s)
- Pedro Serra
- Instituto de Biologia Molecular y Celular de Plantas (UPV-CSIC), Universidad Politécnica de Valencia, Avenida de los Naranjos, 46022 Valencia, Spain
| | - Amber Messmer
- Centre for Plant Health-Sidney Laboratory, Canadian Food Inspection Agency, 8801 East Saanich Road, North Saanich, British Columbia, V8L 1H3, Canada
| | - Daniel Sanderson
- Centre for Plant Health-Sidney Laboratory, Canadian Food Inspection Agency, 8801 East Saanich Road, North Saanich, British Columbia, V8L 1H3, Canada
| | - Delano James
- Centre for Plant Health-Sidney Laboratory, Canadian Food Inspection Agency, 8801 East Saanich Road, North Saanich, British Columbia, V8L 1H3, Canada
| | - Ricardo Flores
- Instituto de Biologia Molecular y Celular de Plantas (UPV-CSIC), Universidad Politécnica de Valencia, Avenida de los Naranjos, 46022 Valencia, Spain.
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49
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Designing fluorescent biosensors using circular permutations of riboswitches. Methods 2018; 143:102-109. [PMID: 29458090 DOI: 10.1016/j.ymeth.2018.02.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 01/31/2018] [Accepted: 02/14/2018] [Indexed: 02/06/2023] Open
Abstract
RNA-based fluorescent (RBF) biosensors have been applied to detect a variety of metabolites in vitro and in live cells. They are designed by combining the ligand sensing domain of natural riboswitches with in vitro selected fluorogenic aptamers. Different biosensor topologies have been developed to accommodate the diversity of riboswitch structures. Here we show that circular permutation of the riboswitch ligand sensing domain also gives functional biosensors, using the SAM-I riboswitch as our model. We reveal that this design can enhance fluorescence turn-on and ligand binding affinity compared to the non-permuted topology.
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50
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Plashkevych O, Li Q, Chattopadhyaya J. How RNase HI (Escherichia coli) promoted site-selective hydrolysis works on RNA in duplex with carba-LNA and LNA substituted antisense strands in an antisense strategy context? MOLECULAR BIOSYSTEMS 2018; 13:921-938. [PMID: 28352859 DOI: 10.1039/c6mb00762g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A detailed kinetic study of 36 single modified AON-RNA heteroduplexes shows that substitution of a single native nucleotide in the antisense strand (AON) by locked nucleic acid (LNA) or by diastereomerically pure carba-LNA results in site-dependent modulation of RNase H promoted cleavage of complementary mRNA strands by 2 to 5 fold at 5'-GpN-3' cleavage sites, giving up to 70% of the RNA cleavage products. The experiments have been performed using RNase HI of Escherichia coli. The 2nd best cleavage site, being the 5'-ApN-3' sites, cleaves up to 23%, depending upon the substitution site in 36 isosequential complementary AONs. A comparison of the modified AON promoted RNA cleavage rates with that of the native AON shows that sequence-specificity is considerably enhanced as a result of modification. Clearly, relatively weaker 5'-purine (Pu)-pyrimidine (Py)-3' stacking in the complementary RNA strand is preferred (giving ∼90% of total cleavage products), which plays an important role in RNase H promoted RNA cleavage. A plausible mechanism of RNase H mediated cleavage of the RNA has been proposed to be two-fold, dictated by the balancing effect of the aromatic character of the purine aglycone: first, the locally formed 9-guanylate ion (pKa 9.3, ∼18-20% N1 ionized at pH 8) alters the adjoining sugar-phosphate backbone around the scissile phosphate, transforming its sugar N/S conformational equilibrium, to preferential S-type, causing preferential cleavage at 5'-GpN-3' sites around the center of 20 mer complementary mRNA. Second, the weaker nearest-neighbor strength of 5'-Pu-p-Py-3' stacking promotes preferential 5'-GpN-3' and 5'-ApN-3' cleavage, providing ∼90% of the total products, compared to ∼50% in that of the native one, because of the cLNA/LNA substituent effect on the neighboring 5'-Pu-p-Py-3' sites, providing both local steric flexibility and additional hydration. This facilitates both the water and water/Mg2+ ion availability at the cleavage site causing sequence-specific hydrolysis of the phosphodiester bond of scissile phosphate. The enhancement of the total rate of cleavage of the complementary mRNA strand by up to 25%, presented in this work, provides opportunities to engineer a single modification site in appropriately substituted AONs to design an effective antisense strategy based on the nucleolytic stability of the AON strand versus RNase H capability to cleave the complementary RNA strand.
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Affiliation(s)
- Oleksandr Plashkevych
- Chemical Biology Program, Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 581, SE-751 23 Uppsala, Sweden.
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