QUANTITATIVE MODELLING OF AUTOPHAGY-RELATED PROTEIN DYNAMICS AND CLUSTERING ON PEROXISOME SURFACES

Abstract

Autophagy is an important process for the degradation of large cellular substrates, such as organelles. Peroxisomes are membrane-bound organelles ranging in size from 0.1-0.8 μm. There can be hundreds of peroxisomes in a single mammalian cell, necessitating regulation of peroxisome numbers, including through degradation by autophagy. Peroxisome autophagy, known as pexophagy, has been shown to be mediated by the common signalling protein ubiquitin, and the autophagy receptor proteins NBR1 and p62. We consider each of ubiquitin, NBR1, and p62 in turn. First, ubiquitin is also involved in the import cycle for peroxisome matrix proteins, and so we quantitatively model the import cycle for systems with ensembles of peroxisomes, each with many import complexes. We consider three different coupling schemes to energetically drive the translocation of matrix proteins across the membrane, and find that our proposed ‘cooperative coupling’ scheme best agrees with existing experimental phenomenology and provides a ubiquitin signal that plausibly signals for peroxisome degradation. Next, NBR1 is the primary autophagy receptor protein for peroxisomes, and recent evidence suggests autophagy receptor proteins can cluster on substrates. Motivated by the possibility of NBR1 clusters on peroxisomes, we model the dynamics of clusters on polydisperse ensembles of spherical drops. The clusters exhibit Lifshitz-Slyozov-Wagner coarsening behaviour, with the cluster scaling function dependent on the drop radius distribution. Large drops are selected for cluster growth, and small drops for cluster evaporation, so that at late times only the largest drops harbour clusters — this suggests that NBR1 clusters may select large peroxisomes for degradation. Finally, adding cluster formation, ubiquitin recruitment of NBR1, and p62 chains on NBR1 and ubiquitin to the model intensifies the selection of large peroxisomes for NBR1 clusters. Overall, we have shown that signalling for peroxisome degradation through autophagy can self-organize in time and to select a subset of peroxisomes for degradation.