Updated project metadata. FtsH zinc metalloproteinases are membrane-intrinsic and occur in bacteria, chloroplasts, and mitochondria. They are involved in diverse cellular processes including protein quality control and regulation. The cyanobacterium Synechocystis possesses four FtsH homologs, designated FtsH1-4 which function as both homo- and hetero-oligomeric complexes. For example, the FtsH1/3 complex is known to have a critical role in iron homeostasis. This project is aimed at the investigation of the involvement of the FtsH1/3 complex in cyanobacterial responses to nitrogen, phosphate and inorganic carbon starvation. By proteomic comparisons of the effects of these nutrient stresses in WT and an FtsH1-down mutant, we demonstrate significant differences in the abundances of transcription factors that complement the responses to nutrient stress at the transcriptome level. We propose a mechanism of epistatic regulation of stress-response gene expression by FtsH1/3 complex-mediated degradation of suppressor transcription factors.