SUMMARY: We present the cpPredictor webserver that implements a novel template-based method for prediction of secondary structure of RNA. The method outperforms available prediction methods as it uses RNA structures of related molecules, either predicted or experimentally identified, as structural templates. The server aims at three major tasks: i) prediction of RNA secondary structures that are difficult to predict by available methods, ii) characterization of uncharacterized RNAs as compatible or incompatible with a chosen template structure and iii) an identification of the most relevant structure among different candidate structures of a single RNA ambiguously predicted by available methods. The web server is accompanied with a comprehensive documentation. AVAILABILITY AND IMPLEMENTATION: The web server is freely available at http://cppredictor.elixir-czech.cz/. The source code of the cpPredictor algorithm is freely available from the webserver under the Apache License, Version 2.0.
To maintain genome integrity, segmented double-stranded RNA viruses of the Reoviridae family must accurately select and package a complete set of up to a dozen distinct genomic RNAs. It is thought that the high fidelity segmented genome assembly involves multiple sequence-specific RNA-RNA interactions between single-stranded RNA segment precursors. These are mediated by virus-encoded non-structural proteins with RNA chaperone-like activities, such as rotavirus (RV) NSP2 and avian reovirus σNS. Here, we compared the abilities of NSP2 and σNS to mediate sequence-specific interactions between RV genomic segment precursors. Despite their similar activities, NSP2 successfully promotes inter-segment association, while σNS fails to do so. To understand the mechanisms underlying such selectivity in promoting inter-molecular duplex formation, we compared RNA-binding and helix-unwinding activities of both proteins. We demonstrate that octameric NSP2 binds structured RNAs with high affinity, resulting in efficient intramolecular RNA helix disruption. Hexameric σNS oligomerizes into an octamer that binds two RNAs, yet it exhibits only limited RNA-unwinding activity compared to NSP2. Thus, the formation of intersegment RNA-RNA interactions is governed by both helix-unwinding capacity of the chaperones and stability of RNA structure. We propose that this protein-mediated RNA selection mechanism may underpin the high fidelity assembly of multi-segmented RNA genomes in Reoviridae.
- MeSH
- Genome, Viral genetics MeSH
- Nucleic Acid Conformation MeSH
- Molecular Chaperones chemistry genetics metabolism MeSH
- Models, Molecular MeSH
- RNA-Binding Proteins chemistry genetics metabolism MeSH
- Orthoreovirus, Avian genetics metabolism MeSH
- RNA, Viral chemistry genetics metabolism MeSH
- Protein Structure, Secondary MeSH
- Base Sequence MeSH
- Protein Binding MeSH
- Viral Nonstructural Proteins chemistry genetics metabolism MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
RNA secondary (2D) structure visualization is an essential tool for understanding RNA function. R2DT is a software package designed to visualize RNA 2D structures in consistent, recognizable, and reproducible layouts. The latest release, R2DT 2.0, introduces multiple significant features, including the ability to display position-specific information, such as single nucleotide polymorphisms or SHAPE reactivities. It also offers a new template-free mode allowing visualization of RNAs without pre-existing templates, alongside a constrained folding mode and support for animated visualizations. Users can interactively modify R2DT diagrams, either manually or using natural language prompts, to generate new templates or create publication-quality images. Additionally, R2DT features faster performance, an expanded template library, and a growing collection of compatible tools and utilities. Already integrated into multiple biological databases, R2DT has evolved into a comprehensive platform for RNA 2D visualization, accessible at https://r2dt.bio.
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 .
- MeSH
- Algorithms MeSH
- Nucleic Acid Conformation MeSH
- RNA chemistry MeSH
- Software * MeSH
- Publication type
- Journal Article MeSH
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 .
- MeSH
- Databases, Nucleic Acid MeSH
- Nucleic Acid Conformation MeSH
- RNA, Untranslated chemistry MeSH
- Reproducibility of Results MeSH
- RNA chemistry MeSH
- Sequence Analysis, RNA MeSH
- Software MeSH
- Computational Biology methods MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Research Support, N.I.H., Intramural MeSH
- Research Support, U.S. Gov't, Non-P.H.S. MeSH
Viral RNA dependent polymerases (vRdPs) are present in all RNA viruses; unfortunately, their sequence similarity is too low for phylogenetic studies. Nevertheless, vRdP protein structures are remarkably conserved. In this study, we used the structural similarity of vRdPs to reconstruct their evolutionary history. The major strength of this work is in unifying sequence and structural data into a single quantitative phylogenetic analysis, using powerful a Bayesian approach. The resulting phylogram of vRdPs demonstrates that RNA-dependent DNA polymerases (RdDPs) of viruses within Retroviridae family cluster in a clearly separated group of vRdPs, while RNA-dependent RNA polymerases (RdRPs) of dsRNA and +ssRNA viruses are mixed together. This evidence supports the hypothesis that RdRPs replicating +ssRNA viruses evolved multiple times from RdRPs replicating +dsRNA viruses, and vice versa. Moreover, our phylogram may be presented as a scheme for RNA virus evolution. The results are in concordance with the actual concept of RNA virus evolution. Finally, the methods used in our work provide a new direction for studying ancient virus evolution.
- MeSH
- Species Specificity MeSH
- Phylogeny MeSH
- Evolution, Molecular * MeSH
- Models, Molecular MeSH
- Molecular Sequence Data MeSH
- RNA-Dependent RNA Polymerase chemistry genetics MeSH
- RNA Viruses classification enzymology genetics MeSH
- Protein Structure, Secondary MeSH
- Amino Acid Sequence MeSH
- Sequence Homology, Amino Acid MeSH
- Protein Structure, Tertiary * MeSH
- Binding Sites genetics MeSH
- Viral Proteins chemistry genetics MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Komplexrií vyšetřování svalových dystrofií pomocí klinických, bioptických a molekulárně genetických diagnostických metod se v naší zemi dosud provádělo pouze ve velmi omezeném rozsahu. Naše skupina (kliiiiků, patologů a genetiků) vyšetřila od roku 1992 do roku 2000 přibližně 240 pacientů suspektních ze svalové dystrofie. Většina pacientů pochází z jihomoravského a severomoravského regionu. Pacienti byli k vyšetření odesíláni zeiména z kUnik a oddělení neurologie a dětské neurologie, dále z odděleni klinické genetiky a méně často z interních klinik a oddělení. Vyšetřovaní pacienti byli podle závěrečné diagnózy rozděleni do skupin pacientů s dystrofinopatií (DMD a BMD), přenašeček dystrofinopatií, pacientů s kongenitální svalovou dystrofií s deficitem merosinu a pacientů s Emery-Dreifussovou svalovou dystrofií, včetně přenašeček tohoto onemocnění. Někteří členové rodin, v nichž se vyskytla dystrofinopatie, byli následně vyšetřeni metodami segregační analýzy. Pacienti DMD/BMD mohou být pomoci molekulárně genetických metod zachyceni ve vysokém procentu. Metoda vyšetření mRŇA pomocí RT PCR a PTT z biopsie dovoluje detegovat delece, duplikace, ale i bodové mutace dystrofinového genu, a tím má vyšší diagnostický rozsah než vyšetření DNA lymfocytů periferní krve metodou multiplex PCR, které zachytí 65 % všech mutací, prakticky jenom delece. Imunofenotypizace dystrofinu se uplatní zejména v odhalování DMD. Deficit sarkolemové reaktivity v karboxytermmální a střední doméně (Dys 1 a Dys 2) jednoznačně signalizuje defektní dystrofiu. Naproti tomu menší deficity dystrofinu u BMD (a též u přenašeček) nemusejí být v biopsii zachyceny. V těchto případech je nutné doplnit vyšetření imunoblotingem nebo analýzou genotypu. Vyšetřování pacientů s klinicky diagnostikovanou svalovou dystrofií by mělo většinou začít vyšetřením biopsie, z níž je možno odhadnout přítomnost a stupeň strukturálních změn, a aplikací protilátek proti DGC případně odhalit patřičný deficit. Imunohistochemické vyšetření je možné doplnit imunoblotingem a tak navést další molekulárně genetické vyšetření DNA či mRNA. Svalovou biopsii je možno v případě deficitu merosinu a emerinu nahradit méně invazivními metodami, jako kožní biopsií nebo výtěrem z bukální sliznice. Při deficitech proteinů DGC je nutno při interpretaci nálezů respektovat možnost sekundární alterace jiných složek, a tak imunohistochemie sama o sobě nemusí být dostatečně informativní. Identifikace a bližší diagnostické zařazení pacientů s deficitem merosinu, sarkoglykanů, emerinu, kalpainu a dalších je možné díky možnosti použití protilátek, které jsou na trhu. Detekce těchto pacientů v naší zemi teprve čeká na jejich soustavné vyhledávání opřené o aplikaci metod popsaných a diskutovaných v tomto sdělení.
Complex diagnosis of muscular dystrophies including clinical, bioptical and molecular genetic approaches has been provided in a limited extent in this country. Our group of neurologists, pathologists and geneticists has examined approximately 240 patients suspected of having muscular dystrophies, mostly coming from Southern and Northern Moravia. The patients were sent to the examination most often firom departments of neurology and clinical genetics, and less firequently fi:om departments of internal medicine. According to the final diagnosis, the patients were divided into groups: with dystrophinopathies and carriers of dystrophinopathies (DMD/BMD), merosin deficient form of congenital muscular dystrophy, and Emery-Dreifuss muscular dystrophy including the carriers of this disease. Some relatives of patients with dystrophinopathies were also examined using the methods of segregation analysis. High proportion of the DMD/BMD patients can be detected by the methods of molecular genetics. Analysis of mRNA using RT PCR and PTT enables the detection of deletions, dupUcations, and point mutations in dystrophin gene and encompasses a larger diagnostic scope in comparison with examinations of DNA level by the multiplex PCR method from the peripheral blood which enables only deletion detections. Immunophenotyping of the dystrophin protein plays an important role especially using antibodies against carboxyterminal (DYS2) and rod domain (DYSl) of dystrophin. Deficient sarcolemmal expression of DYS2 and DYSl reveales unambiguously a pathological dystrophin. On the other hand, less pronounced deficiencies in dystrophin expression in BMD patients and DMD/BMD carriers may not always be detected in muscle biopsies. In this case, it is necessary to supplement the examination by Western blotting and genotype analysis. The examination of patients with clinically diagnosed muscular dystrophy shoidd start with á muscle biopsy which enables the estimation of presence and degree of structural changes. Application of antibodies against the components of DGC and emerin may reveal a deficiency in expression of these proteins. Immunohistochemical examination completed by Western blotting leads to the subsequent molecular genetic analysis of DNA or mRNA. Secondary deficiencies in expression of other DGC proteins are often revealed in muscle biopsies of dystrophinopathies and this fact must be taken into account in the evaluation of immunohistochemical findings. There is a possibility of replacement of invasive muscle biopsy by skin biopsy or buccal mucosal smears in cases of merosin and emerin deficiencies. Commercially available antibodies against merosin, emerin, calpain and sarcoglycans enable extensive identification and detailed classification of muscular dystrophies. Screening of the patients based on the application of methods described and discussed in this report is the task of the forthcoming period.
The crystal structure of the N-terminal domain of the RNA polymerase δ subunit (Nδ) from Bacillus subtilis solved at a resolution of 2.0Å is compared with the NMR structure determined previously. The molecule crystallizes in the space group C222(1) with a dimer in the asymmetric unit. Importantly, the X-ray structure exhibits significant differences from the lowest energy NMR structure. In addition to the overall structure differences, structurally important β sheets found in the NMR structure are not present in the crystal structure. We systematically investigated the cause of the discrepancies between the NMR and X-ray structures of Nδ, addressing the pH dependence, presence of metal ions, and crystal packing forces. We convincingly showed that the crystal packing forces, together with the presence of Ni(2+) ions, are the main reason for such a difference. In summary, the study illustrates that the two structural approaches may give unequal results, which need to be interpreted with care to obtain reliable structural information in terms of biological relevance.
- MeSH
- Bacillus subtilis enzymology MeSH
- DNA-Directed RNA Polymerases chemistry MeSH
- Hydrogen-Ion Concentration MeSH
- Protein Conformation * MeSH
- Crystallography, X-Ray methods MeSH
- Nuclear Magnetic Resonance, Biomolecular methods MeSH
- Protein Structure, Secondary MeSH
- Amino Acid Sequence MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
