text: Chloroplasts have their own genome, which encodes a number of thylakoid proteins. However, during the course of plastid evolution from their cyanobacterial endosymbiotic ancestors, extensive gene transfer from the chloroplast genome to the cell nucleus took place. This results in the four major thylakoid protein complexes being encoded in part by the chloroplast genome and in part by the nuclear genome. Plants have developed several mechanisms to co-regulate the expression of the different subunits encoded in the two different organelles to assure the proper stoichiometry and assembly of these protein complexes. For example, transcription of nuclear genes encoding parts of the photosynthetic apparatus is regulated by light. Biogenesis, stability and turnover of thylakoid protein complexes are regulated by phosphorylation via redox-sensitive kinases in the thylakoid membranes. The translation rate of chloroplast-encoded proteins is controlled by the presence or absence of assembly partners (control by epistasy of synthesis). This mechanism involves negative feedback through binding of excess protein to the 5' untranslated region of the chloroplast mRNA. Chloroplasts also need to balance the ratios of photosystem I and II for the electron transfer chain. The redox state of the electron carrier plastoquinone in the thylakoid membrane directly affects the transcription of chloroplast genes encoding proteins of the reaction centers of the photosystems, thus counteracting imbalances in the electron transfer chain.