The regulation of CCA in F. diplosiphon is controlled by at least one photoreceptor-based signal transduction mechanism. The signal transduction mechanism controlling CCA is termed the Rca (regulator of complementary chromatic adaptation) system. The Rca system is composed of three Rca components: RcaE, RcaF, and RcaC. RcaE is a phytochrome-class photoreceptor that might phosphorylate the response regulators RcaF and RcaC to transcriptionally regulate pcyA, the cpc2 operon, and the cpeC operon. The promoter regions of the cpeC operon, cpc2 operon,and pcyA contain a direct-repeat regulatory element called the L Box (5’TTGCACAN4TTGCACA3’) which is necessary for CCA transcriptional regulation. In red light RcaE might transfer a phosphate to RcaF, which will phosphorylate RcaC, and thus RcaC might bind the L Box more than in green light and acts as a transcriptional activator for pcyA and cpc2, but acts as a repressor for cpeC. A survey of the newly sequenced F. diplosiphon genome has revealed another L Box direct-repeat upstream of an open-reading frame encoding a putative bacteriophytochrome (RcaP).
Bacteriophytochromes are photoreceptors with domains typically consisting of an N-terminal photosensory GAF domain and a C-terminal histidine kinase output domain. The GAF domain typically contains a cysteine that functions as the site for chromophore attachment of a linear open chain tetrapyrrole, such as PCB. However, the domain structure of RcaP differs from typical bacteriophytochromes because it lacks a histidine kinase output domain and has two GAF domains similar to the cyanobacteria phytochrome Cph2 from Synechocystis sp. PCC 6803. Sequence alignments comparing other known photoreceptor GAF domains with RcaP confirm that the RcaP GAF domain contains the conserved cysteine necessary for chromophore attachment in GAF domains of other photoreceptors. The major goals of my research project are to determine whether RcaP is a functional bacteriophytochrome, what the downstream targets of RcaP are, and whether the Rca system regulates this putative bacteriophytochrome through the L Box direct-repeat.