Functional diversification of the cephalopod proteome by RNA-editing

Area of Science:

• Molecular Biology
• Genomics
• Proteomics

Background:

• Coleoid cephalopods possess exceptionally high levels of adenosine deaminase acting on RNA (ADAR)-mediated RNA editing.
• The functional impact of the majority of these recoding events on protein function remains largely uncharacterized.

Purpose of the Study:

• To characterize thousands of recoding events across the Doryteuthis pealeii proteome using integrated proteomics and biochemical assays.
• To elucidate the functional consequences of RNA edit-driven recoding on protein properties and cellular physiology.

Main Methods:

• Quantitative and functional mass spectrometry to analyze the proteome.
• Biochemical and cellular assays to assess protein stability, localization, post-translational modifications, and enzymatic activity.
• Investigation of specific recoding events, such as in the E3 ligase MARCHF5.

Main Results:

• RNA edit-driven recoding significantly alters protein stability, subcellular localization, post-translational modifications, and enzymatic activity.
• Recoding events can create or abolish post-translational modification sites, directly impacting protein function and interactions.
• Recoding of MARCHF5 leads to altered substrate ubiquitylation and disrupts mitochondrial homeostasis.

Conclusions:

• This study provides the first proteome-scale understanding of how extensive RNA recoding diversifies protein function in coleoid cephalopods.
• RNA-level plasticity significantly shapes protein function and cellular physiology, offering a new framework for biological interpretation.