What question did this study set out to answer?

To develop a model-free sequence and structure alignment method integrating high-throughput SHAPE chemical probing data to improve de novo RNA secondary structure modeling.

May 20, 2015PLoS Computational BiologyOpen Access

Model-Free RNA Sequence and Structure Alignment Informed by SHAPE Probing Reveals a Conserved Alternate Secondary Structure for 16S rRNA

View Full Paper

Ask AI

Bookmark

Authors

CLChristopher A. LavenderUniversity of North Carolina at Chapel Hill RLRonny LorenzUniversity of Vienna GZGe ZhangHong Kong Baptist University

Discussion

Member takes

Implication

Comparative structural analysis reveals alternate 16S rRNA secondary conformations across diverse microbes, suggesting dynamic conformational changes drive ribosome function.

Key Points

To develop a model-free sequence and structure alignment method integrating high-throughput SHAPE chemical probing data to improve de novo RNA secondary structure modeling.
Developed a dynamic programming alignment algorithm combining nucleotide sequence identity with SHAPE chemical probing reactivity profiles.
Analyzed protein-free 16S and 23S rRNAs across three evolutionarily diverse organisms: Escherichia coli, Clostridium difficile, and Haloferax volcanii.
Incorporated alignment data and chemical probing reactivities as pseudo-free energy constraints to model consensus ribosomal secondary structures.
Alignments guided solely by SHAPE reactivity reached accuracy levels comparable to sequence-only alignments, with combined sequence and chemical data providing the highest accuracy.
Consensus secondary structure models identified significant deviations from standard accepted models within the functionally critical neck and decoding regions of 16S rRNA.
Demonstrated that 16S rRNA contains conserved alternate base-pairing configurations across bacteria and archaea, indicating large-scale conformational restructuring during protein translation.

Cite This Study

Lavender et al. (2015) studied this question.

synapsesocial.com/papers/6aaf9180d72ef2837f76f1dc https://doi.org/10.1371/journal.pcbi.1004126

View Full Paper

Ask AI

Bookmark

Implication

Comparative structural analysis reveals alternate 16S rRNA secondary conformations across diverse microbes, suggesting dynamic conformational changes drive ribosome function.

Model-Free RNA Sequence and Structure Alignment Informed by SHAPE Probing Reveals a Conserved Alternate Secondary Structure for 16S rRNA

Discussion

Member takes

Implication

Key Points

Cite This Study

Model-Free RNA Sequence and Structure Alignment Informed by SHAPE Probing Reveals a Conserved Alternate Secondary Structure for 16S rRNA

Discussion

Member takes

Implication

Key Points

Cite This Study

Also Consider

Also Consider