Proteases are intimately involved in the control of the cell cycle, gene expression, differentiation, protein targeting and sorting, protein quality control and programmed cell death. Thus, chloroplast proteases are expected to be involved in the regulation of photosynthesis at several different levels as well. However, the role of proteases at most of these levels is still unknown. The development of proplastids and etioplasts into chloroplasts involves not only the synthesis of a new set of proteins, but also massive degradation of the previous population. Gene expression within the chloroplast might require degradation of positive and negative regulators.
Proteases are likely to participate in the biogenetic processes of some protein complexes.
Perhaps the most explored aspect of protein degradation in chloroplasts is its role in adapting to changing environmental conditions. Increasing light intensities lead to photodamage, the repair of which requires accelerated removal of damaged proteins. Adaptation to lower light intensities also involves selective proteolytic degradation. Similarly, heat-denatured proteins that fail to refold properly are probably degraded. Research in chloroplast protein degradation has evolved primarily along two parallel tracks.