Analysis of transcriptome of Chlamydomonas upon ClpP1 depletion and rapamycin treatment

All the proteases and chaperones involved in plastid protein quality control are encoded by the nucleus with exception of the catalytic subunit of the evolutionarily conserved serine-protease ClpP which is essential for the viability of Chlamydomonas cells. To study its function, we have induced a selective gradual depletion of ClpP in this alga which leads to a progressive alteration of chloroplast morphology, causes formation of vesicles and induces extensive cytoplasmic vacuolization, reminiscent of an autophagy phenotype. A high-throughput time-course analysis of the transcriptome and proteome during ClpP depletion revealed a set of proteins that are more abundant at the protein but not at the RNA level upon ClpP depletion which may comprise some of its substrates. Moreover, the specific increase in accumulation, both at the RNA and protein level, of small heat shock proteins, chaperones, proteases and proteins involved in thylakoid maintenance upon perturbation of plastid protein homeostasis suggests the existence of a chloroplast-to-nucleus signaling pathway involved in organelle quality control. Kinetic analysis using deep sequencing of mRNA levels in triplicates upon progressive deletion of ClpP1 protease (0, 12, 31, 43, 48 h) and inhibition of the TOR kinase by rapamycin (0, 2, 8 h).