1
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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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Singh RN, Sani RK. Genome-Wide Computational Prediction and Analysis of Noncoding RNAs in Oleidesulfovibrio alaskensis G20. Microorganisms 2024; 12:960. [PMID: 38792789 PMCID: PMC11124144 DOI: 10.3390/microorganisms12050960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Noncoding RNAs (ncRNAs) play key roles in the regulation of important pathways, including cellular growth, stress management, signaling, and biofilm formation. Sulfate-reducing bacteria (SRB) contribute to huge economic losses causing microbial-induced corrosion through biofilms on metal surfaces. To effectively combat the challenges posed by SRB, it is essential to understand their molecular mechanisms of biofilm formation. This study aimed to identify ncRNAs in the genome of a model SRB, Oleidesulfovibrio alaskensis G20 (OA G20). Three in silico approaches revealed genome-wide distribution of 37 ncRNAs excluding tRNAs in the OA G20. These ncRNAs belonged to 18 different Rfam families. This study identified riboswitches, sRNAs, RNP, and SRP. The analysis revealed that these ncRNAs could play key roles in the regulation of several pathways of biosynthesis and transport involved in biofilm formation by OA G20. Three sRNAs, Pseudomonas P10, Hammerhead type II, and sX4, which were found in OA G20, are rare and their roles have not been determined in SRB. These results suggest that applying various computational methods could enrich the results and lead to the discovery of additional novel ncRNAs, which could lead to understanding the "rules of life of OA G20" during biofilm formation.
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Affiliation(s)
- Ram Nageena Singh
- Department of Chemical and Biological Engineering, South Dakota Mines, Rapid City, SD 57701, USA;
- 2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota Mines, Rapid City, SD 57701, USA
| | - Rajesh K. Sani
- Department of Chemical and Biological Engineering, South Dakota Mines, Rapid City, SD 57701, USA;
- 2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota Mines, Rapid City, SD 57701, USA
- Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota Mines, Rapid City, SD 57701, USA
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3
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Zhang T, Vďačný P. Deciphering phylogenetic relationships of and delimiting species boundaries within the controversial ciliate genus Conchophthirus using an integrative morpho-evo approach. Mol Phylogenet Evol 2024; 190:107931. [PMID: 37742881 DOI: 10.1016/j.ympev.2023.107931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/15/2023] [Accepted: 09/21/2023] [Indexed: 09/26/2023]
Abstract
The phylum Ciliophora (ciliates) comprises about 2600 symbiotic and over 5500 free-living species. The inclusion of symbiotic ciliates in phylogenetic analyses often challenges traditional classification frameworks due to their morphological adaptions to the symbiotic lifestyle. Conchophthirus is such a controversial obligate endocommensal genus whose affinities to other symbiotic and free-living scuticociliates are still poorly understood. Using uni- and multivariate morphometrics as well as 2D-based molecular and phylogenetic analyses, we attempted to test for the monophyly of Conchophthirus, study the boundaries of Conchophthirus species isolated from various bivalves at mesoscale, and reveal the phylogenetic relationships of Conchophthirus to other scuticociliates. Multidimensional analyses of morphometric and cell geometric data generated the same homogenous clusters, as did phylogenetic analyses based on 144 new sequences of two mitochondrial and five nuclear molecular markers. Conchophthirus is not closely related to 'core' scuticociliates represented by the orders Pleuronematida and Philasterida, as assumed in the past using morphological data. Nuclear and mitochondrial markers consistently showed the free-living Dexiotricha and the mouthless endosymbiotic Haptophrya to be the nearest relatives of Conchophthirus. These three highly morphologically and ecologically dissimilar genera represent an orphan clade from the early radiation of scuticociliates in molecular phylogenies.
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Affiliation(s)
- Tengyue Zhang
- Department of Zoology, Comenius University in Bratislava, 842 15 Bratislava, Slovak Republic; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China
| | - Peter Vďačný
- Department of Zoology, Comenius University in Bratislava, 842 15 Bratislava, Slovak Republic.
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4
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Zhang T, Rurik I, Vďačný P. A holistic approach to inventory the diversity of mobilid ciliates (Protista: Ciliophora: Peritrichia). ORG DIVERS EVOL 2023. [DOI: 10.1007/s13127-022-00601-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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5
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Obert T, Zhang T, Rurik I, Vďačný P. First molecular evidence of hybridization in endosymbiotic ciliates (Protista, Ciliophora). Front Microbiol 2022; 13:1067315. [PMID: 36569075 PMCID: PMC9772525 DOI: 10.3389/fmicb.2022.1067315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/14/2022] [Indexed: 12/13/2022] Open
Abstract
Hybridization is an important evolutionary process that can fuel diversification via formation of hybrid species or can lead to fusion of previously separated lineages by forming highly diverse species complexes. We provide here the first molecular evidence of hybridization in wild populations of ciliates, a highly diverse group of free-living and symbiotic eukaryotic microbes. The impact of hybridization was studied on the model of Plagiotoma, an obligate endosymbiont of the digestive tube of earthworms, using split decomposition analyses and species networks, 2D modeling of the nuclear rRNA molecules and compensatory base change analyses as well as multidimensional morphometrics. Gene flow slowed down and eventually hampered the diversification of Lumbricus-dwelling plagiotomids, which collapsed into a single highly variable biological entity, the P. lumbrici complex. Disruption of the species boundaries was suggested also by the continuum of morphological variability in the phenotypic space. On the other hand, hybridization conspicuously increased diversity in the nuclear rDNA cistron and somewhat weakened the host structural specificity of the P. lumbrici complex, whose members colonize a variety of phylogenetically closely related anecic and epigeic earthworms. By contrast, another recorded species, P. aporrectodeae sp. n., showed no signs of introgression, no variability in the rDNA cistron, and very high host specificity. These contrasting eco-evolutionary patterns indicate that hybridization might decrease the alpha-diversity by dissolving species boundaries, weaken the structural host specificity by broadening ecological amplitudes, and increase the nuclear rDNA variability by overcoming concerted evolution within the P. lumbrici species complex.
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Affiliation(s)
| | | | | | - Peter Vďačný
- Department of Zoology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
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6
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Rataj M, Zhang T, Vd’ačný P. Nuclear and Mitochondrial SSU rRNA Genes Reveal Hidden Diversity of Haptophrya Endosymbionts in Freshwater Planarians and Challenge Their Traditional Classification in Astomatia. Front Microbiol 2022; 13:830951. [PMID: 35495648 PMCID: PMC9048206 DOI: 10.3389/fmicb.2022.830951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/18/2022] [Indexed: 11/13/2022] Open
Abstract
Like many other aquatic animals, freshwater planarians have also become partners of symbiotic ciliates from the class Oligohymenophorea. In the present study, we explored the hidden diversity and addressed the questionable systematic position of mouthless obligatory gut endosymbionts of freshwater planarians, using the nuclear and mitochondrial SSU rRNA genes. Although all isolated ciliates morphologically corresponded to a single species, molecular analyses suggested the existence of three genetically distinct entities: Haptophrya planariarum, Haptophrya dugesiarum nov. spec., and Haptophrya schmidtearum nov. spec. The two former species share the same planarian host, which indicates a speciation model involving one duplication event without host switching. Such a diversification pattern was recognized also in astome ciliates inhabiting megascolecid and glossoscolecid earthworms. The present multi-gene phylogenies along with the secondary structure of the mitochondrial 16S rRNA molecule, however, challenge the traditional classification of Haptophrya within the subclass Astomatia. Haptophrya very likely evolved from an orphan scuticociliate lineage by the loss of oral apparatus and by the transformation of the thigmotactic field into an adhesive sucker. Since astomy evolved multiple times independently within the Oligohymenophorea, the loss of cell mouth cannot be used as a sole argument for the assignment of Haptophrya to the Astomatia anymore.
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Affiliation(s)
| | | | - Peter Vd’ačný
- Department of Zoology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
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7
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Das R, Watkins AM. RiboDraw: semiautomated two-dimensional drawing of RNA tertiary structure diagrams. NAR Genom Bioinform 2021; 3:lqab091. [PMID: 34661102 PMCID: PMC8515840 DOI: 10.1093/nargab/lqab091] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 09/06/2021] [Accepted: 10/08/2021] [Indexed: 11/14/2022] Open
Abstract
Publishing, discussing, envisioning, modeling, designing and experimentally determining RNA three-dimensional (3D) structures involve preparation of two-dimensional (2D) drawings that depict critical functional features of the subject molecules, such as noncanonical base pairs and protein contacts. Here, we describe RiboDraw, new software for crafting these drawings. We illustrate the features of RiboDraw by applying it to several RNAs, including the Escherichia coli tRNA-Phe, the P4-P6 domain of Tetrahymena ribozyme, a -1 ribosomal frameshift stimulation element from beet western yellows virus and the 5' untranslated region of SARS-CoV-2. We show secondary structure diagrams of the 23S and 16S subunits of the E. coli ribosome that reflect noncanonical base pairs, ribosomal proteins and structural motifs, and that convey the relative positions of these critical features in 3D space. This software is a MATLAB package freely available at https://github.com/DasLab/RiboDraw.
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Affiliation(s)
- Rhiju Das
- Department of Physics, Stanford University, Stanford, CA 94305, USA
| | - Andrew M Watkins
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
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8
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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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9
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Sweeney BA, Petrov AI, Ribas CE, Finn RD, Bateman A, Szymanski M, Karlowski WM, Seemann SE, Gorodkin J, Cannone JJ, Gutell RR, Kay S, Marygold S, dos Santos G, Frankish A, Mudge JM, Barshir R, Fishilevich S, Chan PP, Lowe TM, Seal R, Bruford E, Panni S, Porras P, Karagkouni D, Hatzigeorgiou AG, Ma L, Zhang Z, Volders PJ, Mestdagh P, Griffiths-Jones S, Fromm B, Peterson KJ, Kalvari I, Nawrocki EP, Petrov AS, Weng S, Bouchard-Bourelle P, Scott M, Lui LM, Hoksza D, Lovering RC, Kramarz B, Mani P, Ramachandran S, Weinberg Z. RNAcentral 2021: secondary structure integration, improved sequence search and new member databases. Nucleic Acids Res 2021; 49:D212-D220. [PMID: 33106848 PMCID: PMC7779037 DOI: 10.1093/nar/gkaa921] [Citation(s) in RCA: 135] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 10/05/2020] [Indexed: 12/16/2022] Open
Abstract
RNAcentral is a comprehensive database of non-coding RNA (ncRNA) sequences that provides a single access point to 44 RNA resources and >18 million ncRNA sequences from a wide range of organisms and RNA types. RNAcentral now also includes secondary (2D) structure information for >13 million sequences, making RNAcentral the world's largest RNA 2D structure database. The 2D diagrams are displayed using R2DT, a new 2D structure visualization method that uses consistent, reproducible and recognizable layouts for related RNAs. The sequence similarity search has been updated with a faster interface featuring facets for filtering search results by RNA type, organism, source database or any keyword. This sequence search tool is available as a reusable web component, and has been integrated into several RNAcentral member databases, including Rfam, miRBase and snoDB. To allow for a more fine-grained assignment of RNA types and subtypes, all RNAcentral sequences have been annotated with Sequence Ontology terms. The RNAcentral database continues to grow and provide a central data resource for the RNA community. RNAcentral is freely available at https://rnacentral.org.
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10
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Sajek MP, Woźniak T, Sprinzl M, Jaruzelska J, Barciszewski J. T-psi-C: user friendly database of tRNA sequences and structures. Nucleic Acids Res 2020; 48:D256-D260. [PMID: 31624839 PMCID: PMC7145666 DOI: 10.1093/nar/gkz922] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 09/30/2019] [Accepted: 10/10/2019] [Indexed: 12/31/2022] Open
Abstract
tRNAs have been widely studied for their role as genetic code decoders in the ribosome during translation, but have recently received new attention due to the discovery of novel roles beyond decoding, often in connection with human diseases. Yet, existing tRNA databases have not been updated for more than a decade, so they do not contain this new functional information and have not kept pace with the rate of discovery in this field. Therefore, a regularly updated database that contains information about newly discovered characteristics of tRNA molecules and can be regularly updated is strongly needed. Here, we report the creation of the T-psi-C database (http://tpsic.igcz.poznan.pl), an up-to-date collection of tRNA sequences that contains data obtained from high-throughput tRNA sequencing, e.g. all isoacceptors and isodecoders for human HEK293 cells. This database also contains 3D tRNA structures obtained from Protein Data Bank and generated using homology modeling. The T-psi-C database can be continuously updated by any member of the scientific community, and contains its own application programming interface (API), which allows users to retrieve or upload data in JSON format. Altogether, T-psi-C is user-friendly, easy to develop and an up-to-date source of knowledge about tRNAs.
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Affiliation(s)
- Marcin Piotr Sajek
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60-479, Poznan, Poland
| | - Tomasz Woźniak
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60-479, Poznan, Poland
| | | | - Jadwiga Jaruzelska
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60-479, Poznan, Poland
| | - Jan Barciszewski
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Noskowskiego 12, 61-704 Poznan, Poland.,NanoBioMedical Centre of the Adam Mickiewicz University, Umultowska 85, 61-614 Poznan, Poland
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11
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RNAcentral: a hub of information for non-coding RNA sequences. Nucleic Acids Res 2020; 47:D221-D229. [PMID: 30395267 PMCID: PMC6324050 DOI: 10.1093/nar/gky1034] [Citation(s) in RCA: 120] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 10/16/2018] [Indexed: 12/11/2022] Open
Abstract
RNAcentral is a comprehensive database of non-coding RNA (ncRNA) sequences, collating information on ncRNA sequences of all types from a broad range of organisms. We have recently added a new genome mapping pipeline that identifies genomic locations for ncRNA sequences in 296 species. We have also added several new types of functional annotations, such as tRNA secondary structures, Gene Ontology annotations, and miRNA-target interactions. A new quality control mechanism based on Rfam family assignments identifies potential contamination, incomplete sequences, and more. The RNAcentral database has become a vital component of many workflows in the RNA community, serving as both the primary source of sequence data for academic and commercial groups, as well as a source of stable accessions for the annotation of genomic and functional features. These examples are facilitated by an improved RNAcentral web interface, which features an updated genome browser, a new sequence feature viewer, and improved text search functionality. RNAcentral is freely available at https://rnacentral.org.
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Affiliation(s)
- The RNAcentral Consortium
http://orcid.org/0000-0002-6497-2883SweeneyBlake Ahttp://orcid.org/0000-0001-7279-2682PetrovAnton IBurkovBorishttp://orcid.org/0000-0001-8626-2148FinnRobert Dhttp://orcid.org/0000-0002-6982-4660BatemanAlexSzymanskiMaciejKarlowskiWojciech MGorodkinJanSeemannStefan ECannoneJamie JGutellRobin RFeyPetraBasuSiddharthaKaySimonhttp://orcid.org/0000-0001-7954-7057CochraneGuyBillisKostantinosEmmertDavidMarygoldSteven Jhttp://orcid.org/0000-0001-6718-3559HuntleyRachael Phttp://orcid.org/0000-0002-9791-0064LoveringRuth CFrankishAdamChanPatricia Phttp://orcid.org/0000-0003-3253-6021LoweTodd Mhttp://orcid.org/0000-0002-8380-5247BrufordElspethSealRuthhttp://orcid.org/0000-0001-6274-0184VandesompeleJohttp://orcid.org/0000-0002-2685-2637VoldersPieter-JanParaskevopoulouMariaMaLinaZhangZhangGriffiths-JonesSamBujnickiJanusz MBoccalettoPietrohttp://orcid.org/0000-0001-8522-334XBlakeJudith ABultCarol JChenRunshengZhaoYiWoodValerieRutherfordKimhttp://orcid.org/0000-0002-2084-269XRivasElenaColeJameshttp://orcid.org/0000-0001-5356-4174LaulederkindStanley J FShimoyamaMaryGillespieMarc EOrlic-MilacicMarijahttp://orcid.org/0000-0001-9424-9197KalvariIoannahttp://orcid.org/0000-0002-2497-3427NawrockiEricEngelStacia Rhttp://orcid.org/0000-0001-9163-5180CherryJ MichaelTeamSILVABerardiniTanya ZHatzigeorgiouArtemisKaragkouniDimitrahttp://orcid.org/0000-0002-1751-9226HoweKevinDavisPaulDingerMarcelhttp://orcid.org/0000-0002-7294-0865HeShunminYoshihamaMakiKenmochiNaoyaStadlerPeter FWilliamsKelly P
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
- Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
- Institute for Cellular and Molecular Biology, and the Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX 78712, USA
- dictyBase, Northwestern University, 420 E. Superior St., Chicago, IL 60611, USA
- Department of Molecular and Cellular Biology, Harvard University, Biological Laboratories, 16 Divinity Avenue, Cambridge, MA 02140, USA
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
- Institute of Cardiovascular Science, University College London, London, UK
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
- DIANA-Lab, Department of Electrical & Computer Engineering, University of Thessaly, 382 21 Volos, Greece
- Hellenic Pasteur Institute, 127 Vasilissis Sofias Avenue, 11521 Athens, Greece
- Ghent University and Cancer Research Institute Ghent, 9000 Ghent, Belgium
- St Vincent's Clinical School, UNSW Sydney, Sydney, Australia
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
- Jackson Laboratory, 600 Main St., Bar Harbor, ME 04609, USA
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100080, China
- Cambridge Systems Biology and Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge, Cambridgeshire CB2 1GA, UK
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
- College of Pharmacy and Health Sciences, St John's University, Queens, NY 11439, USA
- Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
- National Center for Biotechnology Information, U.S. National Library of Medicine, Bethesda, MD 20894, USA
- Department of Biomedical Engineering, Medical College of Wisconsin and Marquette University, Milwaukee, WI 53226, USA
- Department of Genetics, Stanford University, Palo Alto, CA 94304 USA
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, D-28359 Bremen
- Jacobs University Bremen, School of Engineering and Science, D-28759 Bremen
- Frontier Science Research Center, University of Miyazaki, Miyazaki, Japan
- Phoenix Bioinformatics, Fremont, CA 94538, USA
- Systems Biology Department, Sandia National Laboratories, Livermore, CA 94551, USA
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Centre for Bioinformatics, Leipzig University, Härtelstr. 1618, 04107 Leipzig, Germany
- Competence Center for Scalable Data Services and Solutions Dresden/Leipzig, German Centre for Integrative Biodiversity Research (iDiv), and Leipzig Research Center for Civilization Diseases, Universität Leipzig, Ritterstrasse 9–13, 04109 Leipzig, Germany
- Max Planck Institute for Mathematics in the Sciences, Insel Strasse 22, 04103 Leipzig, Germany
- Fraunhofer Institute for Cell Therapy and Immunology, Perlickstrasse 1, 04103 Leipzig, Germany
- Department of Theoretical Chemistry, University of Vienna, Wahringerstrasse 17, 1090 Vienna, Austria
- Center for RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, Frederiksberg C, Denmark
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
- To whom correspondence should be addressed. Tel: +44 1223 492550; Fax: +44 1223 494468;
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12
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Jelínek J, Hoksza D, Hajič J, Pešek J, Drozen J, Hladík T, Klimpera M, Vohradský J, Pánek J. rPredictorDB: a predictive database of individual secondary structures of RNAs and their formatted plots. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2019:5479229. [PMID: 31032840 PMCID: PMC6482342 DOI: 10.1093/database/baz047] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 03/01/2019] [Accepted: 03/21/2019] [Indexed: 12/11/2022]
Abstract
Secondary data structure of RNA molecules provides insights into the identity and function of RNAs. With RNAs readily sequenced, the question of their structural characterization is increasingly important. However, RNA structure is difficult to acquire. Its experimental identification is extremely technically demanding, while computational prediction is not accurate enough, especially for large structures of long sequences. We address this difficult situation with rPredictorDB, a predictive database of RNA secondary structures that aims to form a middle ground between experimentally identified structures in PDB and predicted consensus secondary structures in Rfam. The database contains individual secondary structures predicted using a tool for template-based prediction of RNA secondary structure for the homologs of the RNA families with at least one homolog with experimentally solved structure. Experimentally identified structures are used as the structural templates and thus the prediction has higher reliability than de novo predictions in Rfam. The sequences are downloaded from public resources. So far rPredictorDB covers 7365 RNAs with their secondary structures. Plots of the secondary structures use the Traveler package for readable display of RNAs with long sequences and complex structures, such as ribosomal RNAs. The RNAs in the output of rPredictorDB are extensively annotated and can be viewed, browsed, searched and downloaded according to taxonomic, sequence and structure data. Additionally, structure of user-provided sequences can be predicted using the templates stored in rPredictorDB.
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Affiliation(s)
- Jan Jelínek
- Department of Software Engineering, Faculty of Mathematics and Physics, Charles University, Ke Karlovu, Praha.,Laboratory of Bioinformatics, Institute of Microbiology, The Czech Academy of Sciences, Videnska, Praha
| | - David Hoksza
- Department of Software Engineering, Faculty of Mathematics and Physics, Charles University, Ke Karlovu, Praha.,Luxembourg Centre for Systems Biomedicine, University of Luxembourg, avenue du Swing, Belvaux
| | - Jan Hajič
- Department of Software Engineering, Faculty of Mathematics and Physics, Charles University, Ke Karlovu, Praha
| | - Jan Pešek
- Department of Software Engineering, Faculty of Mathematics and Physics, Charles University, Ke Karlovu, Praha
| | - Jan Drozen
- Department of Software Engineering, Faculty of Mathematics and Physics, Charles University, Ke Karlovu, Praha
| | - Tomáš Hladík
- Department of Software Engineering, Faculty of Mathematics and Physics, Charles University, Ke Karlovu, Praha
| | - Michal Klimpera
- Department of Software Engineering, Faculty of Mathematics and Physics, Charles University, Ke Karlovu, Praha
| | - Jiří Vohradský
- Laboratory of Bioinformatics, Institute of Microbiology, The Czech Academy of Sciences, Videnska, Praha
| | - Josef Pánek
- Laboratory of Bioinformatics, Institute of Microbiology, The Czech Academy of Sciences, Videnska, Praha
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Johnson PZ, Kasprzak WK, Shapiro BA, Simon AE. RNA2Drawer: geometrically strict drawing of nucleic acid structures with graphical structure editing and highlighting of complementary subsequences. RNA Biol 2019; 16:1667-1671. [PMID: 31441369 PMCID: PMC6844559 DOI: 10.1080/15476286.2019.1659081] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 08/19/2019] [Accepted: 08/20/2019] [Indexed: 10/26/2022] Open
Abstract
RNA structure prediction programs remain imperfect and many substructures are still identified by manual exploration, which is most efficiently conducted within an RNA structure drawing program. However, most nucleic acid structure drawing programs have limited capability for structure modification (i.e., breaking and forming new bonds between bases), often requiring that the structure notation be textually edited. RNA2Drawer was developed to allow for graphical structure editing while maintaining the geometry of a drawing (e.g., ellipsoid loops, stems with evenly stacked base pairs) throughout structural changes and manual adjustments to the layout by the user. In addition, the program allows for annotations such as colouring and circling of bases and drawing of tertiary interactions (e.g., pseudoknots). RNA2Drawer can also draw commonly desired elements such as an optionally flattened outermost loop and assists structure editing by automatically highlighting complementary subsequences, which facilitates the discovery of potentially new and alternative pairings, particularly tertiary pairings over long-distances, which are biologically critical in the genomes of many RNA viruses and cannot be accurately predicted by current structure prediction programs. Additionally, RNA2Drawer outputs drawings either as PNG files, or as PPTX and SVG files, such that every object of a drawing (e.g., bases, bonds) is an individual PPTX or SVG object, allowing for further manipulation in Microsoft PowerPoint or a vector graphics editor such as Adobe Illustrator. PowerPoint is the standard for presentations and is often used to create figures for publications, and RNA2Drawer is the first program to export drawings as PPTX files.
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Affiliation(s)
- Philip Z. Johnson
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Wojciech K. Kasprzak
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Bruce A. Shapiro
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Anne E. Simon
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
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Lu JS, Bindewald E, Kasprzak WK, Shapiro BA. RiboSketch: versatile visualization of multi-stranded RNA and DNA secondary structure. Bioinformatics 2019; 34:4297-4299. [PMID: 29912310 DOI: 10.1093/bioinformatics/bty468] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 06/12/2018] [Indexed: 02/02/2023] Open
Abstract
Summary Creating clear, visually pleasing 2D depictions of RNA and DNA strands and their interactions is important to facilitate and communicate insights related to nucleic acid structure. Here we present RiboSketch, a secondary structure image production application that enables the visualization of multistranded structures via layout algorithms, comprehensive editing capabilities, and a multitude of simulation modes. These interactive features allow RiboSketch to create publication quality diagrams for structures with a wide range of composition, size and complexity. The program may be run in any web browser without the need for installation, or as a standalone Java application. Availability and implementation https://rnastructure.cancer.gov/ribosketch.
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Affiliation(s)
- Jacob S Lu
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Eckart Bindewald
- Basic Science Program, RNA Biology Laboratory, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD, USA
| | - Wojciech K Kasprzak
- Basic Science Program, RNA Biology Laboratory, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD, USA
| | - Bruce A Shapiro
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD, USA
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Léger S, Costa MBW, Tulpan D. Pairwise visual comparison of small RNA secondary structures with base pair probabilities. BMC Bioinformatics 2019; 20:293. [PMID: 31142266 PMCID: PMC6542128 DOI: 10.1186/s12859-019-2902-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 05/14/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Predicted RNA secondary structures are typically visualized using dot-plots for base pair binding probabilities and planar graphs for unique structures, such as the minimum free energy structure. These are however difficult to analyze simultaneously. RESULTS This work introduces a compact unified view of the most stable conformation of an RNA secondary structure and its base pair probabilities, which is called the Circular Secondary Structure Base Pairs Probabilities Plot (CS2BP2-Plot). Along with our design we provide access to a web server implementation of our solution that facilitates pairwise comparison of short RNA (and DNA) sequences up to 200 base pairs. The web server first calculates the minimum free energy secondary structure and the base pair probabilities for up to 10 RNA or DNA sequences using RNAfold and then provides a two panel comparative view that includes CS2BP2-Plots along with the traditional graph, planar and circular diagrams obtained with VARNA. The CS2BP2-Plots include highlighting of the nucleotide differences between two selected sequences using ClustalW local alignments. We also provide descriptive statistics, dot-bracket secondary structure representations and ClustalW local alignments for compared sequences. CONCLUSIONS Using circular diagrams and colour and weight-coded arcs, we demonstrate how a single image can replace the state-of-the-art dual representations (dot-plots and minimum free energy structures) for base-pair probabilities of RNA secondary structures while allowing efficient exploration and comparison of different RNA conformations via a web server front end. With that, we provide the community, especially the biologically oriented, with an intuitive tool for ncRNA visualization. Web-server: https://nrcmonsrv01.nrc.ca/cs2bp2plot.
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Affiliation(s)
- Serge Léger
- Digital Technologies Research Center, National Research Council Canada, 100 des Aboiteaux St, Moncton, NB E1A7R1 Canada
| | - Maria Beatriz Walter Costa
- Department of Computer Science, TFome Research Group, Bioinformatics Group, Interdisciplinary Center of Bioinformatics, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany
| | - Dan Tulpan
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario Canada
- Digital Technologies Research Center, National Research Council Canada, 100 des Aboiteaux St, Moncton, NB E1A7R1 Canada
- School of Computer Science, University of Guelph, Guelph, Ontario Canada
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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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