Members of the DegP/HtrA (or Deg) family of proteases are found widely in nature and play an important role in the proteolysis of misfolded and damaged proteins. As yet, their physiological role in oxygenic photosynthetic organisms is unclear, although it has been widely speculated that they participate in the degradation of the photodamaged D1 subunit in the photosystem two complex (PSII) repair cycle, which is needed to maintain PSII activity in both cyanobacteria and chloroplasts. We have examined the role of the three Deg proteases found in the cyanobacterium Synechocystis sp. PCC 6803 through analysis of double and triple insertion mutants. We have discovered that these proteases show overlap in function and are involved in a number of key physiological responses ranging from protection against light and heat stresses to phototaxis. In previous work, we concluded that the Deg proteases played either a direct or an indirect role in PSII repair in a glucose-tolerant version of An inevitable consequence of the light reactions of oxygenic photosynthesis is the formation of highly reactive molecules, such as reactive oxygen species (ROS) 5 and amino acid free radicals, which can cause irreversible damage to a variety of cellular components including nucleic acids, lipids, pigments, and proteins (1, 2). The photosystem two complex (PSII), which functions as the light-driven water:plastoquinone oxidoreductase in oxygenic photosynthetic electron transport, is particularly prone to light-induced damage (3). Of the more than 25 protein subunits found in PSII, the D1 reaction center subunit appears to be the major target for photodamage (4 -6). To maintain activity, a damaged PSII complex is repaired through the specific replacement of the damaged subunit (usually D1) by a newly synthesized subunit (3). Despite the importance of the PSII repair cycle for maintaining optimal photosynthetic rates in vivo, the molecular details of this repair process remain unclear.Recently, attention has focused on the identity of the proteases that are involved in removing damaged D1 from the PSII complex. In the case of chloroplasts, in vitro experiments suggest that D1 degradation occurs in a two-step process involving the participation of two classes of protease (7). First, a member of the DegP/HtrA family of proteases (or Deg proteases), originally designated DegP2 but now renamed Deg2 (8), is thought to cleave damaged D1 between trans-membrane helices four and five on the stromal side of the membrane to generate N-terminal and C-terminal fragments of ϳ23 and 10 kDa, respectively. Subsequently, the 23-kDa fragment, and possibly the 10-kDa fragment, is removed from the membrane by one or more members of the FtsH protease family (9).Selective D1 degradation also occurs in cyanobacteria such as Synechocystis sp. PCC 6803 (10). Analysis of the genome sequence of Synechocystis sp. PCC 6803 has identified three members of the Deg proteases and four members of the FtsH family of proteases (11). Mutagenesis experiments have so far demonstr...