Insights from forward- and chemical-genetic studies on peroxisome functions, peroxisome-environment interactions, and the peroxisome-associated ubiquitination
Doctor of Philosophy
Subcellular compartments (organelles) enclose metabolic pathways to increase enzyme-substrate interactions and prevent leakage of harmful byproducts. The peroxisome is an organelle housing many critical oxidative reactions. In oilseed plants, such as Arabidopsis thaliana, peroxisomes metabolize stored fatty acids to fuel germination and early development. Although a general framework for understanding peroxisome biogenesis is in place, detailed biogenesis mechanisms remain unclear and how peroxisomes respond to environmental challenges is not well understood. Proteins required for peroxisome biogenesis or protein import into the organelle are named peroxins or PEX proteins. PEX5 is a shuttling peroxisomal matrix protein receptor, traveling between the peroxisome and the cytosol. Peroxisome-associated enzymes ubiquitinate PEX5 to signal either return to the cytosol or degradation by the proteasome. I characterized mutants with defective peroxisome-associated ubiquitination machinery and found that mutations in the peroxisome-associated ubiquitin-conjugating enzyme (PEX4) and three RING ubiquitin-protein ligases (PEX2, PEX10, and PEX12) conferred elevated PEX5 levels. Disruption of any Arabidopsis RING peroxin decreased PEX10 levels, indicating that each RING peroxin is required for RING complex stability, as in yeast and mammals. Moreover, reducing PEX4 function in the pex12-1 mutant restored PEX10 levels and partially ameliorated molecular and physiological defects, leading to the hypothesis that PEX4-dependent ubiquitination on the pex12-1 ectopic Lys residue destabilizes the RING peroxin complex in pex12-1. Peroxisomes are dynamic; peroxisomal contents and abundance change to accommodate environmental stimuli, including salinity and high temperature. I found that although growth on high salt promotes peroxisome proliferation, levels of certain peroxisomal proteins were reduced, presumably due to β-oxidation-dependent oxidative stress promoted peroxisomal protein degradation and that catalase protected peroxisomal proteins from degradation. I also found that mildly elevated growth temperature increased proteasomal degradation of PEX5 to reduce overall and detrimental membrane-associated PEX5 levels and alleviated peroxisomal defects in the ubiquitin-conjugating enzyme mutant pex4-1. Overall, this work has increased understanding of individual peroxins and provided insights into peroxisome-environment interactions. I also developed chemical-genetic screens to identify effective chemical modulators of peroxisome functions. Because peroxisome functions and peroxins are highly conserved, these insights and chemical modulators might be useful in peroxisome studies in diverse organisms.