In the facultatively phototrophic proteobacterium Rhodobacter sphaeroides, formation of the photosynthetic apparatus is oxygen dependent. When oxygen tension decreases, the response regulator PrrA of the global two-component PrrBA system is believed to directly activate transcription of the puf, puh, and puc operons, encoding structural proteins of the photosynthetic complexes, and to indirectly upregulate the photopigment biosynthesis genes bch and crt. Decreased oxygen also results in inactivation of the photosynthesis-specific repressor PpsR, bringing about derepression of the puc, bch, and crt operons. We uncovered a hierarchical relationship between these two regulatory systems, earlier thought to function independently. We also more accurately assessed the spectrum of gene targets of the PrrBA system. First, expression of the appA gene, encoding the PpsR antirepressor, is PrrA dependent, which establishes one level of hierarchical dominance of the PrrBA system over AppA-PpsR. Second, restoration of the appA transcript to the wild-type level is insufficient for rescuing phototrophic growth impairment of the prrA mutant, whereas inactivation of ppsR is sufficient. This suggests that in addition to controlling appA transcription, PrrA affects the activity of the AppA-PpsR system via an as yet unidentified mechanism(s). Third, PrrA directly activates several bch and crt genes, traditionally considered to be the PpsR targets. Therefore, in R. sphaeroides, the global PrrBA system regulates photosynthesis gene expression (i) by rigorous control over the photosynthesis-specific AppA-PpsR regulatory system and (ii) by extensive direct transcription activation of genes encoding structural proteins of photosynthetic complexes as well as genes encoding photopigment biosynthesis enzymes.In the facultatively phototrophic alphaproteobacterium Rhodobacter sphaeroides, photosynthesis (PS) operates under anoxic conditions. A decrease in oxygen tension triggers significant upregulation of PS gene transcription (35,38). The photosynthetic apparatus is comprised of the reaction center, encoded by the puh and puf operons, and two light-harvesting complexes, encoded by the puf and puc operons. Enzymes involved in the biosynthesis of photosynthetic pigments, i.e., bacteriochlorophyll a and carotenoids, are encoded by the bch and crt genes, respectively. Most PS-specific genes are located in the R. sphaeroides PS gene cluster, whereas the puc operons are located separately (4, 49). Three major regulatory systems control oxygen-dependent transcription of PS genes. One of these is composed of the antirepressor AppA (15, 17) and the repressor PpsR (7, 36) and is primarily responsible for the regulation of PS genes (30). Two other systems are global regulatory systems, i.e., the redox-responsive two-component system PrrBA (2, 47) and the anaerobic activator FnrL (48).