Mapping the RNA Chaperone Activity of the T. brucei Editosome Using SHAPE Chemical Probing

Leeder, Wolf-Matthias; Hu, Göringer

doi:10.1007/978-1-0716-0231-7_10

Cited by 2 publications

(2 citation statements)

References 36 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…( 14 ). cDNA-fragments were resolved by automated capillary electrophoresis ( 14 , 34 ) and raw electropherograms were processed using ShapeFinder ( 35 ). HRP-data were statistically analyzed using custom Python scripts with the help of forgi 2.0 ( 36 ).…”

Section: Methodsmentioning

confidence: 99%

Fuzzy RNA recognition by theTrypanosoma bruceieditosome

Göringer

2022

Nucleic Acids Research

View full text Add to dashboard Cite

The assembly of high molecular mass ribonucleoprotein complexes typically relies on the binary interaction of defined RNA sequences or precisely folded RNA motifs with dedicated RNA-binding domains on the protein side. Here we describe a new molecular recognition principle of RNA molecules by a high molecular mass protein complex. By chemically probing the solvent accessibility of mitochondrial pre-mRNAs when bound to the Trypanosoma brucei editosome, we identified multiple similar but non-identical RNA motifs as editosome contact sites. However, by treating the different motifs as mathematical graph objects we demonstrate that they fit a consensus 2D-graph consisting of 4 vertices (V) and 3 edges (E) with a Laplacian eigenvalue of 0.5477 (λ2). We establish that synthetic 4V(3E)-RNAs are sufficient to compete for the editosomal pre-mRNA binding site and that they inhibit RNA editing in vitro. Furthermore, we demonstrate that only two topological indices are necessary to predict the binding of any RNA motif to the editosome with a high level of confidence. Our analysis corroborates that the editosome has adapted to the structural multiplicity of the mitochondrial mRNA folding space by recognizing a fuzzy continuum of RNA folds that fit a consensus graph descriptor.

show abstract

Section: Methodsmentioning

confidence: 99%

Fuzzy RNA recognition by theTrypanosoma bruceieditosome

Göringer

2022

Nucleic Acids Research

View full text Add to dashboard Cite

show abstract

“…OH-radical induced phosphodiester cleavage sites were identified by abortive reverse transcription using fluorophore-substituted DNA-primer molecules as described in Leeder et al, 2016a. cDNA-fragments were resolved by automated capillary electrophoresis (Leeder et al, 2016a; Leeder and Göringer 2020) and raw electropherograms were processed using ShapeFinder (Vasa et al, 2008). HRP-data were statistically analyzed using custom Python scripts with the help of forgi 2.0 (Thiel et al, 2019).…”

Section: Methodsmentioning

confidence: 99%

Fuzzy RNA-recognition by theTrypanosoma bruceieditosome

Leeder

2021

Preprint

Self Cite

View full text Add to dashboard Cite

The recognition of RNA-molecules by proteins and protein complexes is a critical step on all levels of gene expression. Typically, the generated ribonucleoprotein complexes rely on the binary interaction of defined RNA-sequences or precisely folded RNA-motifs with dedicated RNA-binding domains on the protein side. Here we describe a new molecular recognition principle of RNA-molecules by a high molecular mass protein complex. By chemically probing the solvent accessibility of mitochondrial pre-mRNAs when bound to the Trypanosoma brucei editosome we identified multiple similar but non-identical RNA-motifs as editosome contact sites. However, by treating the different motifs as mathematical graph objects we demonstrate that they fit a consensus 2D-graph consisting of 4 vertices (V) and 3 edges (E) with a Laplacian eigenvalue of 0.523 (λ2). We establish that a synthetic 4V(3E)-RNA is sufficient to compete for the editosomal pre-mRNA binding site and that it is able to inhibit RNA-editing in vitro. Our analysis corroborates that the editosome has adapted to the structural multiplicity of the mitochondrial mRNA-folding space by recognizing a fuzzy continuum of RNA-folds that fit a consensus graph-descriptor. This provides a mechanism on how the protein complex is able to bind the structurally pleomorphic pool of pre- and partially edited mRNAs. We speculate that other fuzzy RNA-recognition motifs exist especially for proteins that interact with multiple RNA-species.

show abstract

Mapping the RNA Chaperone Activity of the T. brucei Editosome Using SHAPE Chemical Probing

Cited by 2 publications

References 36 publications

Fuzzy RNA recognition by theTrypanosoma bruceieditosome

Fuzzy RNA recognition by theTrypanosoma bruceieditosome

Fuzzy RNA-recognition by theTrypanosoma bruceieditosome

Contact Info

Product

Resources

About