Differential Roles of the Thylakoid Lumenal Deg Protease Homologs in Chloroplast Proteostasis.

Deg proteases are involved in protein quality control in prokaryotes. Of the three Arabidopsis (Arabidopsis thaliana) homologs, Degl, Deg5, and Deg8, located in the thylakoid lumen, Degl forms a homohexamer, whereas Deg5 and Deg8 form a heterocomplex. Both Degl and Deg5-Deg8 were shown separately to degrade photosynthetic proteins during photoinhibition. To investigate whether Degl and Deg5-Deg8 are redundant, a full set of Arabidopsis Deg knockout mutants were generated and their phenotypes were compared. Under all conditions tested, degl mutants were affected more than the wild type and deg5 and deg8 mutants. Moreover, overexpression of Deg5-Deg8 could only partially compensate for the loss of Deg1. Comparative proteomics of degl mutants revealed moderate up-regulation of thylakoid proteins involved in photoprotection, assembly, repair, and housekeeping and down-regulation of those that form photosynthetic complexes. Quantification of protein levels in the wild type revealed that Degl was 2-fold more abundant than Deg5-Deg8. Moreover, recombinant Degl displayed higher in vitro proteolytic activity. Affinity enrichment assays revealed that Degl was precipitated with very few interacting proteins, whereas Deg5-Deg8 was associated with a number of thylakoid proteins, including D1., OECs, LHCBs, Cyt b f, and NDH subunits, thus implying that Deg5-Deg8 is capable of binding substrates but is unable to degrade them efficiently. This work suggests that differences in protein abundance and proteolytic activity underlie the differential importance of Degl and Deg5-Deg8 protease complexes observed in vivo.