STED super-resolution microscopy unveils the dynamics of Atg30 on yeast Pex3-labeled peroxisomes

Eline M F de Lange; Frank N Mol; Ida J van der Klei; Rifka Vlijm

doi:10.1016/j.isci.2024.110481

STED super-resolution microscopy unveils the dynamics of Atg30 on yeast Pex3-labeled peroxisomes

iScience. 2024 Jul 8;27(8):110481. doi: 10.1016/j.isci.2024.110481. eCollection 2024 Aug 16.

Authors

Eline M F de Lange^{1

2}, Frank N Mol², Ida J van der Klei¹, Rifka Vlijm²

Affiliations

¹ Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands.
² Molecular Biophysics, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands.

Abstract

Peroxisomes are dynamic organelles with important metabolic functions. Yeast Pex3 is a multifunctional membrane protein aiding in peroxisomal biogenesis, inheritance, and degradation (pexophagy), by interacting with process-specific factors. Using multicolor (live-cell) stimulated emission depletion (STED) nanoscopy, we studied the localization of Pex3 and its binding partners in Hansenula polymorpha. Unlike confocal microscopy, STED allows resolving the membrane of tiny peroxisomes, enabling accurate measurements of the size of all Pex3-labeled peroxisomes. We localized Pex3 and its binding partners at peroxisome-repressing and -inducing conditions and during pexophagy. In-depth quantitative analysis of Pex3 and pexophagy receptor Atg30 showed dynamic changes in their (co)localization. One remarkable response of Atg30 was the shift in position from being sandwiched between clustered peroxisomes at proliferation conditions, to the cytosolically exposed parts of peroxisome clusters upon pexophagy induction. Summarizing, we show that STED allows characterizing dynamics of the localization of peroxisomal proteins in yeast cells.

Keywords: Biological sciences; Molecular biology; Resolution techniques; Structural biology.