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McCann HM, Meade CD, Banerjee B, Penev PI, Dean Williams L, Petrov AS. RiboVision2: A Web Server for Advanced Visualization of Ribosomal RNAs. J Mol Biol 2024; 436:168556. [PMID: 39237196 DOI: 10.1016/j.jmb.2024.168556] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/24/2024] [Accepted: 03/25/2024] [Indexed: 09/07/2024]
Abstract
RiboVision2 is a web server designed to visualize phylogenetic, structural, and evolutionary properties of ribosomal RNAs simultaneously at the levels of primary, secondary, and three-dimensional structure and in the context of full ribosomal complexes. RiboVision2 instantly computes and displays a broad variety of data; it has no login requirements, is open-source, free for all users, and available at https://ribovision2.chemistry.gatech.edu.
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Affiliation(s)
- Holly M McCann
- NASA Center for the Origin of Life, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA; School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Caeden D Meade
- NASA Center for the Origin of Life, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA; School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Biswajit Banerjee
- NASA Center for the Origin of Life, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA; School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Petar I Penev
- NASA Center for the Origin of Life, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA; School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Loren Dean Williams
- NASA Center for the Origin of Life, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA; School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Anton S Petrov
- NASA Center for the Origin of Life, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA; School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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2
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Johnson PZ, Simon AE. RNAcanvas: interactive drawing and exploration of nucleic acid structures. Nucleic Acids Res 2023:7137443. [PMID: 37094080 DOI: 10.1093/nar/gkad302] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/15/2023] [Accepted: 04/21/2023] [Indexed: 04/26/2023] Open
Abstract
Two-dimensional drawing of nucleic acid structures, particularly RNA structures, is fundamental to the communication of nucleic acids research. However, manually drawing structures is laborious and infeasible for structures thousands of nucleotides long. RNAcanvas automatically arranges residues into strictly shaped stems and loops while providing robust interactive editing features, including click-and-drag layout adjustment. Drawn elements are highly customizable in a point-and-click manner, including colours, fonts, size and shading, flexible numbering, and outlining of bases. Tertiary interactions can be drawn as draggable, curved lines. Leontis-Westhof notation for depicting non-canonical base-pairs is fully supported, as well as text labels for structural features (e.g. hairpins). RNAcanvas also has many unique features and performance optimizations for large structures that cannot be correctly predicted and require manual refinement based on the researcher's own analyses and expertise. To this end, RNAcanvas has point-and-click structure editing with real-time highlighting of complementary sequences and motif search functionality, novel features that greatly aid in the identification of putative long-range tertiary interactions, de novo analysis of local structures, and phylogenetic comparisons. For ease in producing publication quality figures, drawings can be exported in both SVG and PowerPoint formats. URL: https://rnacanvas.app.
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Affiliation(s)
- Philip Z Johnson
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD20742, USA
| | - Anne E Simon
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD20742, USA
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3
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Steger G. Predicting the Structure of a Viroid : Structure, Structure Distribution, Consensus Structure, and Structure Drawing. Methods Mol Biol 2022; 2316:331-371. [PMID: 34845705 DOI: 10.1007/978-1-0716-1464-8_26] [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] [Indexed: 06/13/2023]
Abstract
Viroids are small non-coding RNAs that require a special sequence and structure to be replicated and transported by the host machinery. Many of these features can be predicted and later experimentally verified. Here, we will present workflows to predict viroid structures and draw the predicted structures in a pleasing and descriptive way using recently developed software.
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Affiliation(s)
- Gerhard Steger
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany.
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4
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Sweeney BA, Hoksza D, Nawrocki EP, Ribas CE, Madeira F, Cannone JJ, Gutell R, Maddala A, Meade CD, Williams LD, Petrov AS, Chan PP, Lowe TM, Finn RD, Petrov AI. R2DT is a framework for predicting and visualising RNA secondary structure using templates. Nat Commun 2021; 12:3494. [PMID: 34108470 PMCID: PMC8190129 DOI: 10.1038/s41467-021-23555-5] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 05/04/2021] [Indexed: 02/05/2023] Open
Abstract
Non-coding RNAs (ncRNA) are essential for all life, and their functions often depend on their secondary (2D) and tertiary structure. Despite the abundance of software for the visualisation of ncRNAs, few automatically generate consistent and recognisable 2D layouts, which makes it challenging for users to construct, compare and analyse structures. Here, we present R2DT, a method for predicting and visualising a wide range of RNA structures in standardised layouts. R2DT is based on a library of 3,647 templates representing the majority of known structured RNAs. R2DT has been applied to ncRNA sequences from the RNAcentral database and produced >13 million diagrams, creating the world's largest RNA 2D structure dataset. The software is amenable to community expansion, and is freely available at https://github.com/rnacentral/R2DT and a web server is found at https://rnacentral.org/r2dt .
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Affiliation(s)
- Blake A Sweeney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - David Hoksza
- Department of Software Engineering, Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic
| | - Eric P Nawrocki
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Carlos Eduardo Ribas
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Fábio Madeira
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Jamie J Cannone
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Robin Gutell
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Aparna Maddala
- School of Chemistry and Biochemistry, Center for the Origins of Life, Georgia Institute of Technology, Atlanta, GA, USA
| | - Caeden D Meade
- School of Chemistry and Biochemistry, Center for the Origins of Life, Georgia Institute of Technology, Atlanta, GA, USA
| | - Loren Dean Williams
- School of Chemistry and Biochemistry, Center for the Origins of Life, Georgia Institute of Technology, Atlanta, GA, USA
| | - Anton S Petrov
- School of Chemistry and Biochemistry, Center for the Origins of Life, Georgia Institute of Technology, Atlanta, GA, USA
| | - Patricia P Chan
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Todd M Lowe
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Robert D Finn
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Anton I Petrov
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK.
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5
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Žihala D, Salamonová J, Eliáš M. Evolution of the genetic code in the mitochondria of Labyrinthulea (Stramenopiles). Mol Phylogenet Evol 2020; 152:106908. [PMID: 32702525 DOI: 10.1016/j.ympev.2020.106908] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/30/2020] [Accepted: 07/15/2020] [Indexed: 02/02/2023]
Abstract
Mitochondrial translation often exhibits departures from the standard genetic code, but the full spectrum of these changes has certainly not yet been described and the molecular mechanisms behind the changes in codon meaning are rarely studied. Here we report a detailed analysis of the mitochondrial genetic code in the stramenopile group Labyrinthulea (Labyrinthulomycetes) and their relatives. In the genus Aplanochytrium, UAG is not a termination codon but encodes tyrosine, in contrast to the unaffected meaning of the UAA codon. This change is evolutionarily independent of the reassignment of both UAG and UAA as tyrosine codons recently reported from two uncultivated labyrinthuleans (S2 and S4), which we show are not thraustochytrids as proposed before, but represent the clade LAB14 previously recognised in environmental 18S rRNA gene surveys. We provide rigorous evidence that the UUA codon in the mitochondria of all labyrinthuleans serves as a termination codon instead of encoding leucine, and propose that a sense-to-stop reassignment has also affected the AGG and AGA codons in the LAB14 clade. The distribution of the different forms of sense-to-stop and stop-to-sense reassignments correlates with specific modifications of the mitochondrial release factor mtRF2a in different subsets of labyrinthuleans, and with the unprecedented loss of mtRF1a in Aplanochytrium and perhaps also in the LAB14 clade, pointing towards a possible mechanistic basis of the code changes observed. Curiously, we show that labyrinthulean mitochondria also exhibit a sense-to-sense codon reassignment, manifested as AUA encoding methionine instead of isoleucine. Furthermore, we show that this change evolved independently in the uncultivated stramenopile lineage MAST8b, together with the reassignment of the AGR codons from arginine to serine. Altogether, our study has uncovered novel variants of the mitochondrial genetic code and previously unknown modifications of the mitochondrial translation machinery, further enriching our understanding of the rules governing the evolution of one of the central molecular process in the cell.
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Affiliation(s)
- David Žihala
- Department of Biology and Ecology & Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic
| | - Jana Salamonová
- Department of Biology and Ecology & Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic
| | - Marek Eliáš
- Department of Biology and Ecology & Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic.
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6
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Žihala D, Eliáš M. Evolution and Unprecedented Variants of the Mitochondrial Genetic Code in a Lineage of Green Algae. Genome Biol Evol 2020; 11:2992-3007. [PMID: 31617565 PMCID: PMC6821328 DOI: 10.1093/gbe/evz210] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2019] [Indexed: 12/15/2022] Open
Abstract
Mitochondria of diverse eukaryotes have evolved various departures from the standard genetic code, but the breadth of possible modifications and their phylogenetic distribution are known only incompletely. Furthermore, it is possible that some codon reassignments in previously sequenced mitogenomes have been missed, resulting in inaccurate protein sequences in databases. Here we show, considering the distribution of codons at conserved amino acid positions in mitogenome-encoded proteins, that mitochondria of the green algal order Sphaeropleales exhibit a diversity of codon reassignments, including previously missed ones and some that are unprecedented in any translation system examined so far, necessitating redefinition of existing translation tables and creating at least seven new ones. We resolve a previous controversy concerning the meaning the UAG codon in Hydrodictyaceae, which beyond any doubt encodes alanine. We further demonstrate that AGG, sometimes together with AGA, encodes alanine instead of arginine in diverse sphaeroplealeans. Further newly detected changes include Arg-to-Met reassignment of the AGG codon and Arg-to-Leu reassignment of the CGG codon in particular species. Analysis of tRNAs specified by sphaeroplealean mitogenomes provides direct support for and molecular underpinning of the proposed reassignments. Furthermore, we point to unique mutations in the mitochondrial release factor mtRF1a that correlate with changes in the use of termination codons in Sphaeropleales, including the two independent stop-to-sense UAG reassignments, the reintroduction of UGA in some Scenedesmaceae, and the sense-to-stop reassignment of UCA widespread in the group. Codon disappearance seems to be the main drive of the dynamic evolution of the mitochondrial genetic code in Sphaeropleales.
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Affiliation(s)
- David Žihala
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Czech Republic.,Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Czech Republic
| | - Marek Eliáš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Czech Republic.,Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Czech Republic
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7
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Shabash B, Wiese KC. jViz.RNA 4.0-Visualizing pseudoknots and RNA editing employing compressed tree graphs. PLoS One 2019; 14:e0210281. [PMID: 31059508 PMCID: PMC6502502 DOI: 10.1371/journal.pone.0210281] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 12/19/2018] [Indexed: 11/18/2022] Open
Abstract
Previously, we have introduced an improved version of jViz.RNA which enabled faster and more stable RNA visualization by employing compressed tree graphs. However, the new RNA representation and visualization method required a sophisticated mechanism of pseudoknot visualization. In this work, we present our novel pseudoknot classification and implementation of pseudoknot visualization in the context of the new RNA graph model. We then compare our approach with other RNA visualization software, and demonstrate jViz.RNA 4.0's benefits compared to other software. Additionally, we introduce interactive editing functionality into jViz.RNA and demonstrate its benefits in exploring and building RNA structures. The results presented highlight the new high degree of utility jViz.RNA 4.0 now offers. Users are now able to visualize pseudoknotted RNA, manipulate the resulting automatic layouts to suit their individual needs, and change both positioning and connectivity of the RNA molecules examined. Care was taken to limit overlap between structural elements, particularly in the case of pseudoknots to ensure an intuitive and informative layout of the final RNA structure. Availability: The software is freely available at: https://jviz.cs.sfu.ca/.
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Affiliation(s)
- Boris Shabash
- School of Computing Science, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Kay C. Wiese
- School of Computing Science, Simon Fraser University, Burnaby, British Columbia, Canada
- * E-mail:
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8
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Abstract
Abstract
Motivation
RNA secondary structure is a useful representation for studying the function of RNA, which captures most of the free energy of RNA folding. Using empirically determined energy parameters, secondary structures of nucleic acids can be efficiently computed by recursive algorithms. Several software packages supporting this task are readily available. As RNA secondary structures are outerplanar graphs, they can be drawn without intersection in the plane. Interpretation by the practitioner is eased when these drawings conform to a series of additional constraints beyond outerplanarity. These constraints are the reason why RNA drawing is difficult. Many RNA drawing algorithms therefore do not always produce intersection-free (outerplanar) drawings.
Results
To remedy this shortcoming we propose here the RNApuzzler algorithm which is guaranteed to produce intersection-free drawings. It is based on a drawing algorithm respecting constraints based on nucleotide distances (RNAturtle). We investigate relaxations of these constraints allowing for intersection-free drawings. Based on these relaxations, we implemented a fully automated, simple, and robust algorithm that produces aesthetic drawings adhering to previously established guidelines. We tested our algorithm using the RFAM database and found that we can compute intersection-free drawings of all RNAs therein efficiently.
Availability and implementation
The software can be accessed freely at: https://github.com/dwiegreffe/RNApuzzler.
Supplementary information
Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Daniel Wiegreffe
- Image and Signal Processing Group, Department of Computer Science, Leipzig University, Leipzig, Germany
- Bioinformatics Group, Department of Computer Science, Leipzig University, Leipzig, Germany
| | - Daniel Alexander
- Image and Signal Processing Group, Department of Computer Science, Leipzig University, Leipzig, Germany
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, Leipzig University, Leipzig, Germany
| | - Dirk Zeckzer
- Image and Signal Processing Group, Department of Computer Science, Leipzig University, Leipzig, Germany
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Wiegreffe D, Alexander D, Stadler PF, Zeckzer D. RNApuzzler: efficient outerplanar drawing of RNA-secondary structures. Bioinformatics 2018; 35:1342-1349. [DOI: 10.1093/bioinformatics/bty817] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 08/09/2018] [Accepted: 09/18/2018] [Indexed: 11/12/2022] Open
Affiliation(s)
- Daniel Wiegreffe
- Image and Signal Processing Group, Department of Computer Science, Leipzig University, Leipzig, Germany
- Bioinformatics Group, Department of Computer Science, Leipzig University, Leipzig, Germany
| | - Daniel Alexander
- Image and Signal Processing Group, Department of Computer Science, Leipzig University, Leipzig, Germany
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, Leipzig University, Leipzig, Germany
| | - Dirk Zeckzer
- Image and Signal Processing Group, Department of Computer Science, Leipzig University, Leipzig, Germany
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10
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Elias R, Hoksza D. TRAVeLer: a tool for template-based RNA secondary structure visualization. BMC Bioinformatics 2017; 18:487. [PMID: 29141608 PMCID: PMC5688744 DOI: 10.1186/s12859-017-1885-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 10/31/2017] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Visualization of RNA secondary structures is a complex task, and, especially in the case of large RNA structures where the expected layout is largely habitual, the existing visualization tools often fail to produce suitable visualizations. This led us to the idea to use existing layouts as templates for the visualization of new RNAs similarly to how templates are used in homology-based structure prediction. RESULTS This article introduces Traveler, a software tool enabling visualization of a target RNA secondary structure using an existing layout of a sufficiently similar RNA structure as a template. Traveler is based on an algorithm which converts the target and template structures into corresponding tree representations and utilizes tree edit distance coupled with layout modification operations to transform the template layout into the target one. Traveler thus accepts a pair of secondary structures and a template layout and outputs a layout for the target structure. CONCLUSIONS Traveler is a command-line open source tool able to quickly generate layouts for even the largest RNA structures in the presence of a sufficiently similar layout. It is available at http://github.com/davidhoksza/traveler .
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Affiliation(s)
- Richard Elias
- Faculty of Mathematics and Physics, Charles University, Prague, 11800 Czech Republic
| | - David Hoksza
- Faculty of Mathematics and Physics, Charles University, Prague, 11800 Czech Republic
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11
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Pyle JD, Keeling PJ, Nibert ML. Amalga-like virus infecting Antonospora locustae, a microsporidian pathogen of grasshoppers, plus related viruses associated with other arthropods. Virus Res 2017; 233:95-104. [PMID: 28267607 DOI: 10.1016/j.virusres.2017.02.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 02/18/2017] [Accepted: 02/21/2017] [Indexed: 12/16/2022]
Abstract
A previously reported Expressed Sequence Tag (EST) library from spores of microsporidian Antonospora locustae includes a number of clones with sequence similarities to plant amalgaviruses. Reexamining the sequence accessions from that library, we found additional such clones, contributing to a 3247-nt contig that approximates the length of an amalga-like virus genome. Using A. locustae spores stored from that previous study, and new ones obtained from the same source, we newly visualized the putative dsRNA genome of this virus and obtained amplicons yielding a 3387-nt complete genome sequence. Phylogenetic analyses suggested it as prototype strain of a new genus in family Amalgaviridae. The genome contains two partially overlapping long ORFs, with downstream ORF2 in the +1 frame relative to ORF1 and a proposed motif for +1 ribosomal frameshifting in the region of overlap. Subsequent database searches using the predicted fusion protein sequence of this new amalga-like virus identified related sequences in the transcriptome of a basal hexapod, the springtail species Tetrodontophora bielanensis. We speculate that this second new amalga-like virus (contig length, 3475 nt) likely also derived from a microsporidian, or related organism, which was associated with the springtail specimens at the time of sampling for transcriptome analysis. Other findings of interest include evidence that the ORF1 translation products of these two new amalga-like viruses contain a central region of predicted α-helical coiled coil, as recently reported for plant amalgaviruses, and transcriptome-based evidence for another new amalga-like virus in the transcriptome of another basal hexapod, the two-pronged bristletail species Campodea augens.
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Affiliation(s)
- Jesse D Pyle
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA; Harvard Ph.D. Program in Virology, Division of Medical Sciences, Harvard University, Boston, MA 02115, USA
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Max L Nibert
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA; Harvard Ph.D. Program in Virology, Division of Medical Sciences, Harvard University, Boston, MA 02115, USA.
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12
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Toffano-Nioche C, Gautheret D, Leclerc F. Revisiting the structure/function relationships of H/ACA(-like) RNAs: a unified model for Euryarchaea and Crenarchaea. Nucleic Acids Res 2015; 43:7744-61. [PMID: 26240384 PMCID: PMC4652768 DOI: 10.1093/nar/gkv756] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 07/07/2015] [Accepted: 07/09/2015] [Indexed: 01/22/2023] Open
Abstract
A structural and functional classification of H/ACA and H/ACA-like motifs is obtained from the analysis of the H/ACA guide RNAs which have been identified previously in the genomes of Euryarchaea (Pyrococcus) and Crenarchaea (Pyrobaculum). A unified structure/function model is proposed based on the common structural determinants shared by H/ACA and H/ACA-like motifs in both Euryarchaea and Crenarchaea. Using a computational approach, structural and energetic rules for the guide:target RNA-RNA interactions are derived from structural and functional data on the H/ACA RNP particles. H/ACA(-like) motifs found in Pyrococcus are evaluated through the classification and their biological relevance is discussed. Extra-ribosomal targets found in both Pyrococcus and Pyrobaculum might support the hypothesis of a gene regulation mediated by H/ACA(-like) guide RNAs in archaea.
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Affiliation(s)
- Claire Toffano-Nioche
- I2BC, Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris Sud, 1 avenue de la terrasse, 91198 Gif sur Yvette, France
| | - Daniel Gautheret
- I2BC, Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris Sud, 1 avenue de la terrasse, 91198 Gif sur Yvette, France
| | - Fabrice Leclerc
- I2BC, Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris Sud, 1 avenue de la terrasse, 91198 Gif sur Yvette, France
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