Source 1primary paper2023MED
Toolkit/bioinformatic analysis of ribosome assembly pathway protein components
bioinformatic analysis of ribosome assembly pathway protein components
Taxonomy: Technique Branch / Method. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
This computation method is a bioinformatic analysis applied to protein components of the Saccharomyces cerevisiae ribosome assembly pathway. In the cited study, it compared ribosome biogenesis factors with ribosomal proteins and found that biogenesis factors contain significantly more predicted trans interacting regions.
Usefulness & Problems
Why this is useful
The method is useful for comparative characterization of protein classes within the yeast ribosome assembly pathway using predicted trans interacting regions. It provides a computational way to distinguish ribosome biogenesis factors from ribosomal proteins based on predicted interaction-related sequence features.
Problem solved
It addresses the problem of identifying whether protein components in the Saccharomyces cerevisiae ribosome assembly pathway differ in their predicted trans interacting region content. The cited analysis specifically resolved this comparison between biogenesis factors and ribosomal proteins.
Published Workflows
Objective: Validate and expand a model for how yeast pre-ribosomes are released from the nucleolus into the nucleoplasm.
Why it works: The workflow combines pathway-wide prediction of trans interacting regions in protein components with structural comparison of assembly intermediates, allowing the authors to test whether maturation-associated factor release and rRNA folding reduce theoretical trans-interaction capacity across stages.
rRNA folding due to ribosomal protein bindingrelease of ribosome biogenesis factors from pre-ribosomal particlesreduction of trans interactions below a retention thresholdbioinformatic analysiscryo-EM structure analysis
Stages
- 1.Bioinformatic analysis of ribosome assembly pathway proteins(in_silico_filter)
This stage was performed to validate and expand the idea that trans interactions contribute to nucleolar retention by testing whether RiBi factors are more enriched than ribosomal proteins for predicted trans interacting regions.
Selection: Predicted trans interacting region content in protein components of the Saccharomyces cerevisiae ribosome assembly pathway
- 2.Cryo-EM comparison of nucleolar and post-nucleolar assembly intermediates(functional_characterization)
This stage exists to determine how nucleolar pre-ribosomes differ from post-nucleolar pre-ribosomes and to connect maturation-associated structural changes to reduced nucleolar retention.
Selection: Differences in the capacity of ribosomal proteins, RiBi factors, and rRNA components to interact in trans between nucleolar and post-nucleolar pre-ribosomes
Steps
- 1.Analyze protein components of the Saccharomyces cerevisiae ribosome assembly pathway for predicted trans interacting regionscomputation method
Test whether protein classes in the assembly pathway differ in predicted capacity for trans interactions relevant to nucleolar retention.
The abstract states this was done to validate and expand the initial idea before structural comparison of assembly intermediates.
- 2.Analyze cryo-EM structures of ribosome assembly intermediates to compare nucleolar and post-nucleolar trans-interaction capacitystructural analysis method
Determine how maturation-stage differences in ribosomal proteins, RiBi factors, and rRNA components relate to reduced theoretical trans-interacting capability.
After the protein-class comparison, structural analysis is used to localize how trans-interaction capacity changes across nucleolar and post-nucleolar assembly stages.
Taxonomy & Function
Primary hierarchy
Technique Branch
Method: A concrete computational method used to design, rank, or analyze an engineered system.
Techniques
Computational DesignTarget processes
No target processes tagged yet.
Implementation Constraints
The method was applied to protein components from the Saccharomyces cerevisiae ribosome assembly pathway and relied on prediction of trans interacting regions. No further implementation details are available here regarding software, parameters, training data, or required preprocessing.
The available evidence is limited to a single reported comparative finding from one study in yeast. No details are provided here on the prediction algorithm, input requirements, benchmarking, experimental validation, or performance in other organisms or pathways.
Validation
Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication
Supporting Sources
Ranked Claims
Ribosome biogenesis factors contain significantly more predicted trans interacting regions than ribosomal proteins in the Saccharomyces cerevisiae ribosome assembly pathway.
We found that ribosome biogenesis factors (RiBi factors) contain significantly more predicted trans interacting regions than RPs.
Ribosome biogenesis factors contain significantly more predicted trans interacting regions than ribosomal proteins in the Saccharomyces cerevisiae ribosome assembly pathway.
We found that ribosome biogenesis factors (RiBi factors) contain significantly more predicted trans interacting regions than RPs.
Ribosome biogenesis factors contain significantly more predicted trans interacting regions than ribosomal proteins in the Saccharomyces cerevisiae ribosome assembly pathway.
We found that ribosome biogenesis factors (RiBi factors) contain significantly more predicted trans interacting regions than RPs.
Ribosome biogenesis factors contain significantly more predicted trans interacting regions than ribosomal proteins in the Saccharomyces cerevisiae ribosome assembly pathway.
We found that ribosome biogenesis factors (RiBi factors) contain significantly more predicted trans interacting regions than RPs.
Ribosome biogenesis factors contain significantly more predicted trans interacting regions than ribosomal proteins in the Saccharomyces cerevisiae ribosome assembly pathway.
We found that ribosome biogenesis factors (RiBi factors) contain significantly more predicted trans interacting regions than RPs.
Ribosome biogenesis factors contain significantly more predicted trans interacting regions than ribosomal proteins in the Saccharomyces cerevisiae ribosome assembly pathway.
We found that ribosome biogenesis factors (RiBi factors) contain significantly more predicted trans interacting regions than RPs.
Ribosome biogenesis factors contain significantly more predicted trans interacting regions than ribosomal proteins in the Saccharomyces cerevisiae ribosome assembly pathway.
We found that ribosome biogenesis factors (RiBi factors) contain significantly more predicted trans interacting regions than RPs.
Ribosome biogenesis factors contain significantly more predicted trans interacting regions than ribosomal proteins in the Saccharomyces cerevisiae ribosome assembly pathway.
We found that ribosome biogenesis factors (RiBi factors) contain significantly more predicted trans interacting regions than RPs.
Approval Evidence
1 source1 linked approval claimfirst-pass slug bioinformatic-analysis-of-ribosome-assembly-pathway-protein-components
To validate and expand on this idea, we performed a bioinformatic analysis of the protein components of the Saccharomyces cerevisiae ribosome assembly pathway.
Source:
comparative analysissupports
Ribosome biogenesis factors contain significantly more predicted trans interacting regions than ribosomal proteins in the Saccharomyces cerevisiae ribosome assembly pathway.
We found that ribosome biogenesis factors (RiBi factors) contain significantly more predicted trans interacting regions than RPs.
Source:
Comparisons
Source-backed strengths
The reported strength is that it yielded a significant comparative result in Saccharomyces cerevisiae, showing enrichment of predicted trans interacting regions in ribosome biogenesis factors relative to ribosomal proteins. The evidence supports use as a hypothesis-generating computational analysis for pathway component comparison.
Source:
We found that ribosome biogenesis factors (RiBi factors) contain significantly more predicted trans interacting regions than RPs.
Ranked Citations
- 1.