Green/red light-sensing mechanism in the chromatic acclimation photosensor

Abstract

Certain cyanobacteria alter their photosynthetic light absorption between green and red, a phenomenon called complementary chromatic acclimation. The acclimation is regulated by a cyanobacteriochrome-class photosensor that reversibly photoconverts between green-absorbing (Pg) and red-absorbing (Pr) states. Here, we elucidated the structural basis of the green/red photocycle. In the Pg state, the bilin chromophore adopted the extended C15-Z,anti structure within a hydrophobic pocket. Upon photoconversion to the Pr state, the bilin is isomerized to the cyclic C15-E,syn structure, forming a water channel in the pocket. The solvation/desolvation of the bilin causes changes in the protonation state and the stability of π-conjugation at the B ring, leading to a large absorption shift. These results advance our understanding of the enormous spectral diversity of the phytochrome superfamily.

Fig. 1.. Crystal structure of RcaE in the deprotonated Pg state.

(A) Overall structures of the GAF domain in the Pg state (Protein Data Bank ID 8K9O). The PCB chromophore is shown in cyan. The α face and β face of the PCB are indicated by arrows. A corresponding topology diagram of the four α helices and four β sheets is also shown. (B) F_obs, F_calc (observed and calculated structure factors) map of PCB contoured at 2.5σ. (C) Detailed interactions of PCB and residues in the GAF domain. The putative hydrogen bond network is shown as dashed lines.

Fig. 2.. Structural changes during the green/red photocycle.

(A) Positional difference of the Cα atoms of the residues 165 to 312 (black circles) between the Pg (8K9O) and Pr (7CKV) states. B factors for 500-ns MD simulation of the Pg (pink) state and Pr (blue) states are shown. (B) Comparison of crystal structures of the Pg (pink) and Pr (blue) states. PCB is in the C15-Z,anti structure (cyan) in the Pg state and the C15-E,syn structure (yellow) in the Pr state. Water molecules in the water channels are shown as red balls. The hydrogen bond network is shown as dashed lines. (C) Structural change around the wind-up helix and solvent-gate sheet. PCB and water molecules in the channel are shown as lines and red balls, respectively. (D) Structural change in the protein surface between the Pg and Pr states. The water channel connecting the solvent to PCB is formed only in the Pr state.

Fig. 3.. Identification of the bilin deprotonation site.

(A) 1D NMR spectra of RcaE reconstituted with ¹⁵N-labeled PCBs uniformly (top) and specifically for B ring (middle) or C ring (bottom) in the Pg state. Signals of deprotonated (pink) and protonated (blue) nitrogens are shown accordingly. The structure of the B ring deprotonated C-15Z,anti bilin in the Pg state is shown. (B) Comparison of absorption spectra (top) and circular dichroism spectra (bottom) for calculated (left) and experimental (right) data in the Pg (pink) and Pr (blue) states. (C) Bond lengths of the four pyrrole rings were calculated for structures of the Pg-B (pink) and Pr (blue) models. Typical CC bond lengths for single (ethane, 1.531 Å), conjugated double (benzene, 1.397 Å), and double (ethene, 1.331 Å) bonds are indicated as dotted lines.