Egy2 belong to site-2 proteases. Proteases of these type are integral membrane proteins able to perform the proteolytic cleavage within the cell membrane and are thought to participate in signal transduction pathways by releasing of membrane-anchored transcription factors in a process called regulated intramembrane proteolysis (RIP). The Egy2 protein is known to be proteolytically active and located in thylakoid membranes. Its physiological function remain, however, elusive and its substrates remains unknown. Using the reverse genetic approach, we have investigated the consequences of absence of Egy2 proteases for Arabidopsis thaliana chloroplasts. The analysis were performed on two separate Arabidopsis thaliana mutant lines with T-DNA insertion in Egy2 encoding gene. Both Arabidopsis thaliana egy2 mutant lines display changes in expression level of chloroplast genes located on two operons PSBA and PSBC/ PSBD. We observed a significant increase in abundance of PsbA transcript and reduced accumulation level of PsbD and PsbC transcripts. The observed changes in gene expression correlated with changes in abundance of proteins encoded by these genes. In both Arabidopsis thaliana egy2 mutant lines accumulation of PsbA protein was observed as well as decreased accumulation level of PsbC and PsbD genes. The analysis of thylakoid membranes proteome revealed that the absence of Egy2 protease leads to accumulation pTAC10, pTAC16 and FLN1 proteins. These proteins are known as associating with core complex of plastid encoded RNA polymerase and influencing its transcriptional activity. The RNA polymerase in turn is responsible for transcription PSBA and PSBC/PSBD operons. Thus, results support the hypothesis that FLN1, pTAC10 and pTAC16 are substrates for Egy2 protease and participate in regulation of expression PSBA and PSBC/PSBD operons.