The membrane-intrinsic Zn-metalloproteinase FtsH4 does not associate with FtsH1, FtsH2 or FtsH3 but does interact with the uncharacterized protein Sll1106

FtsH Zn-metalloproteinases are multimeric, membrane-intrinsic and universally conserved in bacteria, chloroplasts and mitochondria. FtsHs function in protein turnover and processing: activities that are essential in maintaining cellular homeostasis. In phototrophic organisms, FtsHs are additionally involved in the biogenesis and repair of the photosystem complexes. The cyanobacterium Synechocystis synthesizes 4 homologous FtsHs: FtsH1, 2, 3, and 4. While the first 3 are known to function as hetero-oligomers FtsH1/3 and FtsH2/3, interactions involving FtsH4 are not fully characterized. Here, we determined the relative amounts of the 4 FtsHs in wild-type Synechocystis thylakoid membranes using the iBAQ method. In conjunction with FLAG-affinity pulldown experiments, FtsH4 was found not to associate with the other FtsHs. However, the uncharacterized protein Sll1106 was identified as an FtsH interaction partner.