RiboVision suite for visualization and analysis of ribosomes

Bernier, Chad R.; Petrov, Anton S.; Waterbury, Chris C.; Jett, James R.; Li, Fengbo; Freil, Larry; Xiong, Xin; Wang, Lan; Migliozzi, Blacki Li Rudi; Hershkovits, Eli; Xue, Yuan; Hsiao, Chiaolong; Bowman, Jessica C.; Harvey, Stephen C.; Grover, Martha A.; Wartell, Zachary; Williams, Loren Dean

doi:10.1039/c3fd00126a

Cited by 108 publications

(106 citation statements)

References 38 publications

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“…C80%/U20%. A80%/C18%)[8]. In crystal structures of S. cerevisiae[58] (pdb 3u5b, 3.0 Ǻ resolution) ribosomes and cryoEM structures of human ribosomes[59] (pdb 3j3f, 5 Ǻ resolution), the T+loop backbone structure is similar to that of prokaryotes (Figure 7), and some base orientations vary.…”

Section: Discussionmentioning

confidence: 99%

“…Twelve of the 58 GAC nucleobases are completely conserved throughout all kingdoms (Figure 1), but those sites that vary (and co-vary) allow substitutions to be introduced and tested for structure/function. In particular, position 1061 is 58% uridine, 36% guanine, and 6% adenine[8]. Curiously, the distribution largely follows phylogenetic classifications: uridine is found in eubacteria, guanine in eukaryotes, and some archaebacteria have adenine.…”

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confidence: 99%

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Nucleobases Undergo Dynamic Rearrangements during RNA Tertiary Folding

Welty

Hall

2016

Journal of Molecular Biology

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The tertiary structure of the GTPase Center (GAC) of 23S rRNA as seen in cocrystals is extremely compact. It is stabilized by long-range hydrogen bonds and nucleobase stacking, and a triloop that forms within its 3-way junction. Its folding pathway from secondary structure to tertiary structure has not been previously observed, but it was shown in equilibrium experiments to require Mg2+ ions. The fluorescent nucleotide 2-aminopurine was substituted at selected sites within the 60 nucleotide GAC. Fluorescence intensity changes upon addition of MgCl2 were monitored over a time-course from 1 ms to 100 s as the RNA folds. The folding pathway is revealed here to be hierarchical through several intermediates. Observation of the nucleobases during folding provides a new perspective on the process and the pathway, revealing the dynamics of nucleobase conformational exchange during the folding transitions.

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Section: Discussionmentioning

confidence: 99%

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confidence: 99%

Nucleobases Undergo Dynamic Rearrangements during RNA Tertiary Folding

Welty

Hall

2016

Journal of Molecular Biology

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“…The margins between the phases are somewhat indistinct, and the original LSU phases (10) were adjusted slightly here to account for data from the SSU. Secondary structures of LSU and SSU rRNAs are taken from our public gallery (apollo.chemistry.gatech.edu/RibosomeGallery/), and data are mapped by the web server RiboVision (23). 3D analysis of ancestral expansion was performed using the 70S ribosome of E. coli (Protein Data Bank ID code 4V9D) (25).…”

Section: Methodsmentioning

confidence: 99%

History of the ribosome and the origin of translation

Petrov

Gulen

Norris

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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We present a molecular-level model for the origin and evolution of the translation system, using a 3D comparative method. In this model, the ribosome evolved by accretion, recursively adding expansion segments, iteratively growing, subsuming, and freezing the rRNA. Functions of expansion segments in the ancestral ribosome are assigned by correspondence with their functions in the extant ribosome. The model explains the evolution of the large ribosomal subunit, the small ribosomal subunit, tRNA, and mRNA. Prokaryotic ribosomes evolved in six phases, sequentially acquiring capabilities for RNA folding, catalysis, subunit association, correlated evolution, decoding, energy-driven translocation, and surface proteinization. Two additional phases exclusive to eukaryotes led to tentacle-like rRNA expansions. In this model, ribosomal proteinization was a driving force for the broad adoption of proteins in other biological processes. The exit tunnel was clearly a central theme of all phases of ribosomal evolution and was continuously extended and rigidified. In the primitive noncoding ribosome, proto-mRNA and the small ribosomal subunit acted as cofactors, positioning the activated ends of tRNAs within the peptidyl transferase center. This association linked the evolution of the large and small ribosomal subunits, protomRNA, and tRNA.RNA evolution | translation | origin of life | A-minor interactions T he ribosome retains interpretable molecular records of a world of primordial molecules (1) from around 4 billion years ago (2-9). The records are maintained in rRNA secondary and 3D structures, which are fully conserved throughout the tree of life, and in rRNA sequences, which are more variable (SI Appendix, Fig. S1). Here we use information within ribosomes from each major branch of the tree of life to reconstruct much of the emergence of the universal translational machinery. Large Ribosomal Subunit EvolutionPreviously, we reported a 3D comparative method that revealed a molecular level chronology of the evolution of the large ribosomal subunit (LSU) rRNA (10). Insertion fingerprints are evident when comparing 3D structures of LSU rRNAs of various sizes from various species. These insertion fingerprints mark sites where rRNA expands, recording growth steps on a molecular level.Within the common core of the LSU rRNA, insertion fingerprints were used to identify ancient growth sites. We showed that insertion fingerprints provide a roadmap from the first steps in the formation of the peptidyl transferase center (PTC) (10) located in the ancient heart of the LSU (2-6), culminating in the common core.Small Ribosomal Subunit, LSU, tRNA, and mRNA Evolution Here, using the 3D comparative method, we establish a comprehensive and coherent model for the evolution of the entire ribosome. This model covers the LSU rRNA, small ribosomal subunit (SSU) rRNA, tRNA, and mRNA. The evolution of each of these components is reconciled at the molecular level to a common chronology. This evolutionary model, which we call the "accretion model," ...

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“…Bernier et al [9], for instance, used a combination of 1D plots, 2D sequence diagrams, and 3D visualizations for the visual analysis of RNA structures in ribosomes. We directly encode the information in the color of the abstracted representations.…”

Section: Related Workmentioning

confidence: 99%

Multiscale Visualization and Scale-Adaptive Modification of DNA Nanostructures

Miao

Llano

Sorger

et al. 2018

IEEE Trans. Visual. Comput. Graphics

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Abstract-We present an approach to represent DNA nanostructures in varying forms of semantic abstraction, describe ways to smoothly transition between them, and thus create a continuous multiscale visualization and interaction space for applications in DNA nanotechnology. This new way of observing, interacting with, and creating DNA nanostructures enables domain experts to approach their work in any of the semantic abstraction levels, supporting both low-level manipulations and high-level visualization and modifications. Our approach allows them to deal with the increasingly complex DNA objects that they are designing, to improve their features, and to add novel functions in a way that no existing single-scale approach offers today. For this purpose we collaborated with DNA nanotechnology experts to design a set of ten semantic scales. These scales take the DNA's chemical and structural behavior into account and depict it from atoms to the targeted architecture with increasing levels of abstraction. To create coherence between the discrete scales, we seamlessly transition between them in a well-defined manner. We use special encodings to allow experts to estimate the nanoscale object's stability. We also add scale-adaptive interactions that facilitate the intuitive modification of complex structures at multiple scales. We demonstrate the applicability of our approach on an experimental use case. Moreover, feedback from our collaborating domain experts confirmed an increased time efficiency and certainty for analysis and modification tasks on complex DNA structures. Our method thus offers exciting new opportunities with promising applications in medicine and biotechnology.

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RiboVision suite for visualization and analysis of ribosomes

Cited by 108 publications

References 38 publications

Nucleobases Undergo Dynamic Rearrangements during RNA Tertiary Folding

Nucleobases Undergo Dynamic Rearrangements during RNA Tertiary Folding

History of the ribosome and the origin of translation

Multiscale Visualization and Scale-Adaptive Modification of DNA Nanostructures

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