Selective accumulation of matrix proteins inside of peroxisomal subdomains

Abstract

Formation of specialized reaction spaces prevents interference between distinct cellular pathways. Peroxisomes are cellular compartments involved in a large diversity of metabolic processes. How peroxisomes differentiate into subpopulations and by which mechanism intraorganellar domains are formed remains largely elusive. Here, we report on enzymes from the fungus Ustilago maydis, which accumulate inside of peroxisomal subdomains. We describe a short peptide motif (Tyr-Ile-Ile-Val) sufficient to trigger focal localization. Mining for proteins with similar motifs uncovered several peroxisomal matrix proteins that accumulate in intraorganellar foci. These foci are enriched in the enzyme urate oxidase – a typical constituent of the paracrystalline core of peroxisomes. Upon peroxisome proliferation uneven distribution of focal structures results in the formation of peroxisome subpopulations with different protein content. The underlying principle of subdomain formation is evolutionary conserved in mammalian peroxisomes and formation of similar foci was also observed inside of mitochondria. We propose that peroxisomal proteins show an individual propensity to self-assemble. This formation of protein aggregates appears to be a ubiquitous driving force to spatially organize the peroxisomal proteome.

The peroxisome: an update on mysteries 3.0

“…While confocal microscopy of human fibroblasts expressing a GFP-tagged matrix protein (SCP2) shows typical homogeneous peroxisomal staining, applying STED microscopy reveals the signal to be heterogeneously and sometimes asymmetrically distributed within the bounds of the peroxisomal membrane (Galiani et al 2016 ). This selective accumulation of proteins within subdomains of the peroxisomal matrix has been further interrogated in the fungus Ustilago maydis (Ast et al 2022 ). Using the super-resolution technique of structured illumination microscopy (SIM), specific matrix enzymes in a subpopulation of peroxisomes are seen to localise to small foci within the lumen, which only partially colocalise with typical fluorescent matrix markers.…”

“…Using the super-resolution technique of structured illumination microscopy (SIM), specific matrix enzymes in a subpopulation of peroxisomes are seen to localise to small foci within the lumen, which only partially colocalise with typical fluorescent matrix markers. The presence of the short peptide motif TIIV at the N-terminus of imported proteins is reportedly sufficient to recruit them to these foci within the matrix, likely representing the crystalline core structure, in both U. maydis and mammalian cells (Ast et al 2022 ). The functional significance of this remains to be seen, but it may be a mechanism to generate different subpopulations of peroxisomes with unique protein content and thus specialised functions (Ast et al 2022 ).…”

“…The presence of the short peptide motif TIIV at the N-terminus of imported proteins is reportedly sufficient to recruit them to these foci within the matrix, likely representing the crystalline core structure, in both U. maydis and mammalian cells (Ast et al 2022 ). The functional significance of this remains to be seen, but it may be a mechanism to generate different subpopulations of peroxisomes with unique protein content and thus specialised functions (Ast et al 2022 ).…”