ORCID IDs: 0000-0003-1718-9121 (Y.K.); 0000-0001-9747-5042 (W.S.).Chloroplasts originated from the endosymbiosis of ancestral cyanobacteria and maintain transcription and translation machineries for around 100 proteins. Most endosymbiont genes, however, have been transferred to the host nucleus, and the majority of the chloroplast proteome is composed of nucleus-encoded proteins that are biosynthesized in the cytosol and then imported into chloroplasts. How chloroplasts and the nucleus communicate to control the plastid proteome remains an important question. Protein-degrading machineries play key roles in chloroplast proteome biogenesis, remodeling, and maintenance. Research in the past few decades has revealed more than 20 chloroplast proteases, which are localized to specific suborganellar locations. In particular, two energy-dependent processive proteases of bacterial origin, Clp and FtsH, are central to protein homeostasis. Processing endopeptidases such as stromal processing peptidase and thylakoidal processing peptidase are involved in the maturation of precursor proteins imported into chloroplasts by cleaving off the amino-terminal transit peptides. Presequence peptidases and organellar oligopeptidase subsequently degrade the cleaved targeting peptides. Recent findings have indicated that not only intraplastidic but also extraplastidic processive protein-degrading systems participate in the regulation and quality control of protein translocation across the envelopes. In this review, we summarize current knowledge of the major chloroplast proteases in terms of type, suborganellar localization, and diversification. We present details of these degradation processes as case studies according to suborganellar compartment (envelope, stroma, and thylakoids). Key questions and future directions in this field are discussed.Over 1 billion years of plastid evolution since the endosymbiosis of ancestral cyanobacteria (Douzery et al., 2004), chloroplast biogenesis has gained complexity, with large sets of the endosymbiont genes being transferred to host nuclear genomes. While only 100 endosymbiont genes remain in the plastid genome, with the corresponding proteins biosynthesized there, the nuclear genes have often gained complexity by duplication and diversification of the original endosymbiotic genes. This complexity raises numerous questions regarding (1) at what level gene expression is coordinately controlled, (2) what molecules coordinate the cross talk between chloroplasts and the nucleus, (3) how proteins get across membranes and become imported into chloroplasts, and (4) how the stoichiometries of nucleus-and chloroplast-encoded subunits within individual chloroplast protein complexes such as photosystems and Rubisco are strictly maintained.Given these questions, chloroplast biogenesis has remained a central subject in plant physiology for the last few decades (Jarvis and López-Juez, 2013). In our view, the aforementioned questions point to the importance of protein homeostasis and posttranslational modificat...