Parkin's Substrate Targeting Region Mediates Preferential Ubiquitination of the Mitochondrial GTPase Miro1

Grunnleggende konsepter

Parkin, an E3 ubiquitin ligase, preferentially ubiquitinates the mitochondrial GTPase Miro1 through a conserved substrate targeting region in its linker domain.

Sammendrag

The content explores the substrate recognition mechanism of the E3 ubiquitin ligase Parkin. Key highlights:

1. Untagged, full-length Parkin activated by phosphorylation can ubiquitinate a variety of proteins, but exhibits a strong preference for the mitochondrial GTPase Miro1 in a mix of substrates.

2. Despite the low affinity of the interaction, the authors were able to capture a Parkin-Miro1 complex using chemical crosslinking. This allowed them to identify a conserved substrate targeting region (STR) within the linker domain of Parkin that is crucial for binding to Miro1.

3. Computational modeling using AlphaFold predicted the STR region in Parkin to interact with a hydrophobic pocket in the EF1 domain of Miro1. Disrupting this interaction, either by mutating key residues or by competing with a synthetic STR-containing peptide, compromised Miro1 ubiquitination by Parkin.

4. The authors propose that the STR-mediated Parkin-Miro1 interaction allows Parkin to be pre-positioned at the mitochondrial membrane, primed for rapid activation and ubiquitination of Miro1 upon mitochondrial damage, which is an important step in the mitophagy process.

Statistikk

Parkin can ubiquitinate a variety of proteins, including Miro1, Mfn1, mitoNEET, ubiquitin, UBE2L3, and the FANCI/FANCD2 complex.
Parkin exhibits a strong preference for ubiquitinating Miro1 compared to other substrates.
The Parkin I122Y mutant and the Miro1 L221R mutant show decreased complex formation and Miro1 ubiquitination by Parkin.

Sitater

"Parkin in its active conformation can modify many proteins that contain solvent-exposed lysines."
"Miro1 is the preferred substrate of pParkin, even compared to Ub or Parkin itself, in a mix of substrates."
"Our findings uncover a substrate recognition mechanism in Parkin and explain previous observations in mitophagy in cells."

Viktige innsikter hentet fra

A substrate-interacting region of Parkin directs ubiquitination of the mitochondrial GTPase Miro1

by Koszela,J., ... klokken www.biorxiv.org 06-03-2024

https://www.biorxiv.org/content/10.1101/2024.06.03.597144v1

Dypere Spørsmål

How might the STR-mediated Parkin-Miro1 interaction be regulated in cells to control the timing and specificity of Miro1 ubiquitination during mitophagy?

The STR-mediated Parkin-Miro1 interaction could be regulated in cells through various mechanisms to control the timing and specificity of Miro1 ubiquitination during mitophagy. One possible regulatory mechanism is post-translational modifications (PTMs) of either Parkin or Miro1. Phosphorylation, for example, is a common PTM that can modulate protein-protein interactions. Phosphorylation of Parkin or Miro1 at specific sites within or near the STR region could enhance or inhibit their interaction, thereby regulating Miro1 ubiquitination. Additionally, the expression levels of Parkin and Miro1 could be regulated in response to cellular signals or stress conditions, influencing the availability of the proteins for interaction.
Furthermore, the cellular localization of Parkin and Miro1 could play a role in regulating their interaction. For instance, the recruitment of Parkin to damaged mitochondria, where Miro1 is located, could facilitate their interaction and subsequent ubiquitination. Regulatory proteins or cofactors may also modulate the Parkin-Miro1 interaction by stabilizing or disrupting the complex.
Overall, the timing and specificity of Miro1 ubiquitination by Parkin during mitophagy could be finely tuned by a combination of PTMs, protein expression levels, cellular localization, and regulatory proteins to ensure efficient and selective targeting of Miro1 for degradation.

How might the STR-mediated Parkin-Miro1 interaction be regulated in cells to control the timing and specificity of Miro1 ubiquitination during mitophagy?

The STR-mediated Parkin-Miro1 interaction could be regulated in cells through various mechanisms to control the timing and specificity of Miro1 ubiquitination during mitophagy. One possible regulatory mechanism is post-translational modifications (PTMs) of either Parkin or Miro1. Phosphorylation, for example, is a common PTM that can modulate protein-protein interactions. Phosphorylation of Parkin or Miro1 at specific sites within or near the STR region could enhance or inhibit their interaction, thereby regulating Miro1 ubiquitination. Additionally, the expression levels of Parkin and Miro1 could be regulated in response to cellular signals or stress conditions, influencing the availability of the proteins for interaction.
Furthermore, the cellular localization of Parkin and Miro1 could play a role in regulating their interaction. For instance, the recruitment of Parkin to damaged mitochondria, where Miro1 is located, could facilitate their interaction and subsequent ubiquitination. Regulatory proteins or cofactors may also modulate the Parkin-Miro1 interaction by stabilizing or disrupting the complex.
Overall, the timing and specificity of Miro1 ubiquitination by Parkin during mitophagy could be finely tuned by a combination of PTMs, protein expression levels, cellular localization, and regulatory proteins to ensure efficient and selective targeting of Miro1 for degradation.

How might the STR-mediated Parkin-Miro1 interaction be regulated in cells to control the timing and specificity of Miro1 ubiquitination during mitophagy?

The STR-mediated Parkin-Miro1 interaction could be regulated in cells through various mechanisms to control the timing and specificity of Miro1 ubiquitination during mitophagy. One possible regulatory mechanism is post-translational modifications (PTMs) of either Parkin or Miro1. Phosphorylation, for example, is a common PTM that can modulate protein-protein interactions. Phosphorylation of Parkin or Miro1 at specific sites within or near the STR region could enhance or inhibit their interaction, thereby regulating Miro1 ubiquitination. Additionally, the expression levels of Parkin and Miro1 could be regulated in response to cellular signals or stress conditions, influencing the availability of the proteins for interaction.
Furthermore, the cellular localization of Parkin and Miro1 could play a role in regulating their interaction. For instance, the recruitment of Parkin to damaged mitochondria, where Miro1 is located, could facilitate their interaction and subsequent ubiquitination. Regulatory proteins or cofactors may also modulate the Parkin-Miro1 interaction by stabilizing or disrupting the complex.
Overall, the timing and specificity of Miro1 ubiquitination by Parkin during mitophagy could be finely tuned by a combination of PTMs, protein expression levels, cellular localization, and regulatory proteins to ensure efficient and selective targeting of Miro1 for degradation.