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Updated: Jan 31, 2026

An Optimized Quantitative Pull-Down Analysis of RNA-Binding Proteins Using Short Biotinylated RNA
Published on: February 17, 2023
Mutually exclusive binding of PP1 and RNA to AKAP149 affects the mitochondrial network
Marie Rogne1, Anne Jorunn Stokka, Kjetil Taskén
11Institute of Basic Medical Sciences, Department of Biochemistry, University of Oslo, Post Box 1112, Blindern, 0317 Oslo, Norway.
Abstract:
A-kinase-anchoring protein 149 (AKAP149) is a membrane protein of the mitochondrial and endoplasmic reticulum/nuclear envelope network. AKAP149 controls the subcellular localization and temporal order of protein phosphorylation by tethering protein kinases and phosphatases to these compartments. AKAP149 also includes an RNA-binding K homology (KH) domain, the loss of function of which has been associated in other proteins with neurodegenerative syndromes. We show here that protein phosphatase 1 (PP1) binding occurs through a conserved RVXF motif found in the KH domain of AKAP149 and that PP1 and RNA binding to this same site is mutually exclusive and controlled through a novel, phosphorylation-dependent mechanism. A collapse of the mitochondrial network is observed upon introduction of RNA-binding deficient mutants of AKAP149, pointing to the importance of RNA tethering to the mitochondrial membrane by AKAP149 for mitochondrial distribution.
Insights
A-kinase-anchoring protein 149 (AKAP149) tethers protein kinases and phosphatases to cellular membranes. Its RNA-binding function is crucial for maintaining mitochondrial network structure, with disruptions leading to collapse.
Area of Science:
- Cell Biology
- Molecular Biology
- Neuroscience
Background:
- A-kinase-anchoring protein 149 (AKAP149) is a key scaffolding protein regulating protein phosphorylation at the mitochondria and endoplasmic reticulum/nuclear envelope.
- AKAP149 possesses an RNA-binding K homology (KH) domain, mutations in which are linked to neurodegenerative diseases in other proteins.
Purpose of the Study:
- To investigate the mechanism of protein phosphatase 1 (PP1) binding to AKAP149.
- To elucidate the interplay between PP1 binding, RNA binding, and phosphorylation within the AKAP149 KH domain.
- To determine the role of AKAP149's RNA-binding function in mitochondrial morphology and distribution.
Main Methods:
- Biochemical assays to identify the PP1 binding site on AKAP149.
- Mutagenesis studies to assess the impact of altered RNA-binding or PP1-binding motifs.
- Cellular imaging techniques to observe mitochondrial network structure in response to AKAP149 mutants.
Main Results:
- PP1 binds to AKAP149 via a conserved RVXF motif within the KH domain.
- PP1 binding and RNA binding to the KH domain are mutually exclusive and regulated by phosphorylation.
- AKAP149 mutants deficient in RNA binding cause mitochondrial network collapse, highlighting the importance of RNA tethering for mitochondrial distribution.
Conclusions:
- AKAP149's KH domain acts as a regulatory hub for both protein phosphatase 1 interaction and RNA binding.
- Phosphorylation-dependent control of this hub dictates the functional state of AKAP149.
- AKAP149-mediated RNA tethering to mitochondria is essential for maintaining mitochondrial network integrity.
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