Signal amplification and transduction in phytochrome photosensors

Abstract

Sensory proteins must relay structural signals from the sensory site over large distances to regulatory output domains. Phytochromes are a major family of red-light sensing kinases that control diverse cellular functions in plants, bacteria, and fungi.1-9 Bacterial phytochromes consist of a photosensory core and a C-terminal regulatory domain.10,11 Structures of photosensory cores are reported in the resting state12-18 and conformational responses to light activation have been proposed in the vicinity of the chromophore.19-23 However, the structure of the signalling state and the mechanism of downstream signal relay through the photosensory core remain elusive. Here, we report crystal and solution structures of the resting and active states of the photosensory core of the bacteriophytochrome from Deinococcus radiodurans. The structures reveal an open and closed form of the dimeric protein for the signalling and resting state, respectively. This nanometre scale rearrangement is controlled by refolding of an evolutionarily conserved “tongue”, which is in contact with the chromophore. The findings reveal an unusual mechanism where atomic scale conformational changes around the chromophore are first amplified into an Ångström scale distance change in the tongue, and further grow into a nanometre scale conformational signal. The structural mechanism is a blueprint for understanding how the sensor proteins connect to the cellular signalling network.

Crystal structure of the photosensing module from a red/far-red light-absorbing plant phytochrome

“…Conversion of the hairpin from β-stranded to helical then impacts the OPM by reversibly altering the GAF/ PHY domain connections. This β-strand to helical refolding was recently confirmed by low-resolution paired Pr and Pfr crystal structures of the PSM from Dr-BphP, which in turn, supported a large-scale separation of the sister PHY domains within the dimer (29). Our analyses of Arabidopsis PhyB support this model for Phys with PAS/GAF/PHY domain architectures and extend it to other PSM features that promote the Pr/Pfr transitions and stabilize the two end states (Fig.…”

“…Together, these effects presumably melt the GAF/ hairpin interaction, including the D307/R582 salt bridge, to permit helical refolding of the stem. As proposed (7,29), this refolding also would swivel the main-chain positions of the melted strands-β ent and -β exit with respect to the GAF domain and swap the positions of R582 and S584 to now allow hydrogen bonding between S584 and D307 (Fig. 5).…”

Engineering adenylate cyclases regulated by near-infrared window light

“…S1). These distances turned out to fit nicely in the 10-40 Å spread between the α-helices of the Deinococcus BphP in the dark and lit states (41). Whether proteins whose homodimers are separated by larger distances can be made light-responsive is unclear.…”

“…Our demonstration that homodimeric bacteriophytochromes are amenable to protein engineering (24) and recent progress in structural understanding of dark-to-light conformational changes (41) should encourage design of new NIRW light-activated proteins. Because activities of many signal transduction components depend on homodimerization, including membrane receptors, cyclic nucleotide phosphodiesterases, certain protein phosphatases, proteases, nucleases, and transcription factors, we expect significant expansion of the optogenetic toolset involving NIRW light.…”

“…The NIRW light-activated ACs, IlaCs, constructed in this study, are consistent with our assumption. The recently solved structures of the photosensory module of the Deinoccoccus bacteriophytochrome showed that the distance between the tips of the signaling α-helices changes by as much as ∼30 Å in response to light (41).…”