MultiSETTER: web server for multiple RNA structure comparison

Čech, Petr; Hoksza, David; Svozil, Daniel

doi:10.1186/s12859-015-0696-8

Cited by 10 publications

(7 citation statements)

References 43 publications

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“…Identical nucleotides are blocked in black. Structural superimposition of mitochondrial (red) and bacterial (amber) SRL RNA tertiary structures was performed with the web server MultiSETTER [42] uploading PDB files (human 16S mt‐rRNA, PDB ID: 3J7Y; E. coli 23S SRL, PDB ID: 1Q9A) as input ( S ‐distance 0.209, P ‐value 0.039). (B) Cleavage products generated following mtVapC20 expression were analysed by high‐resolution northern blot as described.…”

Section: Resultsmentioning

confidence: 99%

Messenger RNA delivery to mitoribosomes – hints from a bacterial toxin

2020

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In mammalian mitochondria, messenger RNA is processed and matured from large primary transcripts in structures known as RNA granules. The identity of the factors and process transferring the matured mRNA to the mitoribosome for translation is unclear. Nascent mature transcripts are believed to associate initially with the small mitoribosomal subunit prior to recruitment of the large subunit to form the translationally active monosome. When the small subunit fails to assemble, however, the stability of mt-mRNA is only marginally affected, and under these conditions, the LRPPRC/SLIRP RNA-binding complex has been implicated in maintaining mt-mRNA stability. Here, we exploit the activity of a bacterial ribotoxin, VapC20, to show that in the absence of the large mitoribosomal subunit, mt-mRNA species are selectively lost. Further, if the small subunit is also depleted, the mt-mRNA levels are recovered. As a consequence of these data, we suggest a natural pathway for loading processed mt-mRNA onto the mitoribosome.

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Section: Resultsmentioning

confidence: 99%

Messenger RNA delivery to mitoribosomes – hints from a bacterial toxin

2020

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“…Structural alignment is necessary for this purpose, since, homologous RNAs from different organisms have slightly different sequence and structure and consequently have different residue numbering. We have used SETTER [32][33][34][35] algorithm for structural alignment of RNAs. For the purpose of 3D structural alignment, SETTER (SEcondary sTructure-based TERtiary Structure Similarity Algorithm) divides an RNA structure into a set of nonoverlapping structural elements called generalized secondary structure units (GSSUs).…”

Section: Tools and Methodsmentioning

confidence: 99%

Reverse Watson-Crick purine-purine base pairs — the Sharp-turn motif and other structural consequences in functional RNAs

Mittal¹,

Halder²,

Bhattacharya³

et al. 2017

Preprint

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Identification of static and/or dynamic roles of different noncanonical base pairs is essential for a comprehensive understanding of the sequence-structure-function space of RNA. In this context, reverse WatsonCrick purine-purine base pairs (A:A, G:G & A:G W:W Trans) constitute an interesting class of noncanonical base pairs in RNA due to their characteristic C1 -C1 distance (highest among all base pairing geometries) and parallel local strand orientation. Structural alignment of the RNA stretches containing these W:W Trans base pairs with their corresponding homologous sites in a non-redundant set of RNA crystal structures show that, as expected, these base pairs are associated with specific structural folds or functional roles. Detailed analysis of these contexts further revealed a bimodal distribution in the local backbone geometry parameters associated with these base pairs. One mode, populated by both A:A and G:G W:W Trans pairs, manifests itself as a characteristic backbone fold. We call this fold a 'Sharp-turn' motif. The other mode is exclusively associated with A:A W:W Trans pairs involved in mediating higher order interactions. The same trend is also observed in available solution NMR structures. We have also characterized the importance of recurrent hydrogen bonding interactions between adenine and guanine in W:W Trans geometry. Quantum chemical calculations performed at M05-2X/6-31++(2d,2p) level explain how the characteristic electronic properties of these W:W Trans base pairs facilitate their occurrence in such exclusive structural folds that are important for RNA functionalities.

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“…[52][53][54] The design model and the experimentally-refined model were aligned and compared using the MultiSETTER web tool for RNA structure comparison. [55] 3D Variability Analysis: 3DVA was performed in cryoSPARC using particle stacks from the first round of 3D classification. The classes that resembled the PXT and not the junk classes were used as an input for 3DVA.…”

Section: Methodsmentioning

confidence: 99%

An RNA Paranemic Crossover Triangle as A 3D Module for Cotranscriptional Nanoassembly

Vallina

McRae

Geary

et al. 2022

Small

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RNA nanotechnology takes advantage of structural modularity to build self‐assembling nano‐architectures with applications in medicine and synthetic biology. The use of paranemic motifs, that form without unfolding existing secondary structure, allows for the creation of RNA nanostructures that are compatible with cotranscriptional folding in vitro and in vivo. In previous work, kissing‐loop (KL) motifs have been widely used to design RNA nanostructures that fold cotranscriptionally. However, the paranemic crossover (PX) motif has not yet been explored for cotranscriptional RNA origami architectures and information about the structural geometry of the motif is unknown. Here, a six base pair‐wide paranemic RNA interaction that arranges double helices in a perpendicular manner is introduced, allowing for the generation of a new and versatile building block: the paranemic‐crossover triangle (PXT). The PXT is self‐assembled by cotranscriptional folding and characterized by cryogenic electron microscopy, revealing for the first time an RNA PX interaction in high structural detail. The PXT is used as a building block for the construction of multimers that form filaments and rings and a duplicated PXT motif is used as a building block to self‐assemble cubic structures, demonstrating the PXT as a rigid self‐folding domain for the development of wireframe RNA origami architectures.

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MultiSETTER: web server for multiple RNA structure comparison

Cited by 10 publications

References 43 publications

Messenger RNA delivery to mitoribosomes – hints from a bacterial toxin

Messenger RNA delivery to mitoribosomes – hints from a bacterial toxin

Reverse Watson-Crick purine-purine base pairs — the Sharp-turn motif and other structural consequences in functional RNAs

An RNA Paranemic Crossover Triangle as A 3D Module for Cotranscriptional Nanoassembly

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