Functional Characterization of a Cyanobacterial OmpR/PhoB Class Transcription Factor Binding Site Controlling Light Color Responses

Complementary chromatic acclimation (CCA) allows many cyanobacteria to change the composition of their light-harvesting antennae for maximal absorption of different wavelengths of light. In the freshwater species Fremyella diplosiphon, this process is controlled by the ratio of red to green light and allows the differential regulation of two subsets of genes in the genome. This response to ambient light color is controlled in part by a two-component system that includes a phytochrome class photoreceptor and a response regulator with an OmpR/PhoB class DNA binding domain called RcaC. During growth in red light, RcaC is able to simultaneously activate expression of red light-induced genes and repress expression of green light-induced genes through binding to the L box promoter element. Here we investigate how the L box functions as both an activator and a repressor under the same physiological conditions by analyzing the effects of changing the position, orientation, and sequence of the L box. We demonstrate that changes in the local sequences surrounding the L box affect the strength of its activity and that the activating and repressing functions of the L box are orientation dependent. Also, the spacing between the L box and the transcription start site is critical for it to work as an activator, while its repressing role during light regulation requires additional upstream and downstream DNA sequence elements. The latter result suggests that the repressing function of RcaC requires it to operate in association with multiple additional DNA binding proteins, at least one of which is functioning as an activator. Cyanobacteria possess the ability to modify their photosynthetic light-harvesting antennae, or phycobilisomes (PBS), in response to changes in a wide range of abiotic cues, including both light intensity and color (20–22). Color responsiveness is called chromatic acclimation. This process is widespread in marine and freshwater environments and exists in multiple forms, the best characterized of which is called complementary chromatic acclimation (CCA; historically referred to as “adaptation”) (15, 30, 38, 44). The model organism for the study of CCA and its regulation is the freshwater filamentous cyanobacterium Fremyella diplosiphon UTEX 481/Tolypothrix sp. PCC 7601. During CCA, PBS production in this organism is influenced by the ratio of green light (GL) to red light (RL) in the environment. Growth in RL leads to the accumulation of two different forms of an RL-absorbing chromoprotein called phycocyanin (PC) in the outer regions of the PBS. These two forms are called PC1 and PC2. Growth in GL results in the accumulation of PC1 and another chromoprotein, called phycoerythrin (PE), which maximally absorbs GL, in the outer portions of the PBS. Thus, cyanobacteria that are capable of CCA can maximize photon capture for photosynthesis by tailoring the color absorption profiles of their PBS to the spectral distribution of ambient light in the green and red regions of the spectrum. CCA-controlled changes in PC2 and PE abundance have so far been found to occur entirely at the level of transcription. Transcripts from the cpcB2A2H2I2D2 operon (hereafter called the cpc2 operon), which encodes the PC2 apoproteins as well