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Related Concept Videos

Ribosomal RNA Synthesis02:53

Ribosomal RNA Synthesis

Ribosome synthesis is a highly complex and coordinated process involving more than 200 assembly factors. The synthesis and processing of ribosomal components occurs not only in the nucleolus but also in the nucleoplasm and the cytoplasm of eukaryotic cells.
Ribosome biogenesis begins with the synthesis of 5S and 45S pre-rRNAs by distinct RNA polymerases. The primary transcripts are extensively processed and modified before they are bound and folded by ribosomal proteins and assembly factors,...
Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...

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Quantitative Proteomics Using Reductive Dimethylation for Stable Isotope Labeling
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Streamlining Protein Fractional Synthesis Rates Using SP3 Beads and Stable Isotope Mass Spectrometry: A Case Study on

Dione Gentry-Torfer1,2, Ester Murillo3, Chloe L Barrington4,5

  • 1Applied Metabolome Analysis, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.

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|May 13, 2024
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Summary
This summary is machine-generated.

This study introduces an optimized method for profiling riboproteomes and measuring ribosomal protein synthesis rates using mass spectrometry. The approach enables detailed analysis of ribosomal protein abundance, modifications, and dynamics, advancing our understanding of ribosome function.

Keywords:
Bottom-up proteomicsFractional protein synthesis ratesRibo-proteomeSP3 beadsTop-down proteomics

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Area of Science:

  • Molecular Biology
  • Proteomics
  • Biochemistry

Background:

  • Ribosomes are essential ribonucleoprotein complexes with context-dependent functions influenced by ribosomal protein (r-protein) rearrangements, analogous to the histone code.
  • Current omics methods for riboproteome analysis often involve harsh denaturation and digestion, limiting insights into post-translational modifications (PTMs) and dynamic assembly.
  • Understanding r-protein stoichiometry and synthesis is crucial for linking ribosomal structure to function, a gap addressed by advanced proteomic techniques.

Purpose of the Study:

  • To develop and optimize a method for profiling the riboproteome and determining r-protein synthesis rates across various organisms.
  • To enable the characterization of r-protein abundances, PTMs, and fractional synthesis rates using a milder, reversible denaturation approach.
  • To provide a computational tool (R package ProtSynthesis) for accurate analysis of protein fractional synthesis rates.

Main Methods:

  • A novel method for purifying riboproteomes using reversible denaturation with GuHCl, preserving PTMs.
  • Combined top-down and bottom-up proteomics strategies for detailed r-protein analysis.
  • Stable isotope-assisted mass spectrometry to determine fractional synthesis rates, with corrections for physiological parameters.

Main Results:

  • The optimized method allows for efficient purification of the riboproteome and accurate calculation of fractional synthesis rates.
  • The approach successfully profiles individual r-protein abundances, PTM status, and dynamic assembly into ribosomal complexes.
  • The R package ProtSynthesis provides a validated tool for studying protein synthesis rates under varying physiological conditions.

Conclusions:

  • This holistic methodology offers a significant advancement in understanding the dynamic native state of the r-proteome, bridging the gap between high-resolution structures and functional insights.
  • The method is applicable to various macromolecular assemblies beyond ribosomes, provided efficient purification protocols exist.
  • The study provides a comprehensive approach for investigating ribosome function and translational control, particularly demonstrated in plants.