Control of protein accumulation by LON2 peroxisomal protease and autophagy

Peroxisomes are membrane-bound eukaryotic organelles that house essential metabolic pathways. Many of these pathways generate damaging reactive oxygen species (ROS) that also function as signaling molecules. In Arabidopsis thaliana, damaged or obsolete peroxisomal proteins can be degraded by the LON2 peroxisomal protease. In addition, peroxisomes can be entirely degraded through a specialized form of autophagy (pexophagy), a process that is amplified when LON2 is dysfunctional. As a first step towards surveying the transcriptional landscape of dysfunctional LON2 , we used RNA-seq analysis to compare transcript that are induced and reduced when LON2 is dysfunctional in the presence and absence of autophagy. RNA-seq of 6 day old continuous light grown whole seeding extract of Arabidopsis wild type Col-0 (3 biological replicates) as a control, atg2-4 mututant (3 biological replicates), lon2-8 mutant (3 biological replicates), lon2-8 atg2-4 double mutant (3 biological replicates).