Mapping light-driven conformational changes within the photosensory module of plant phytochrome B

Abstract

Organisms developed different photoreceptors to be able to adapt to changing environmental light conditions. Phytochromes are red/far-red (r/fr) photochromic photoreceptors that belong to the classical photoreceptors along with cryptochromes and phototropins. They convert absorbed light into a biological signal by switching between two states in a light-dependent manner therefore enabling the light control downstream signalling. Their Pfr conformation is the biological active form in plants, but until now only a structure of the ground state (Pr) was solved. Here, the authors provide information about structural changes occurring during photoconversion within phytochrome B and identify possible interaction sites for its N-terminal extension (NTE) utilising hydrogen/deuterium exchange rate analyses of its amide backbone. Especially, the newly identified light-dependency of two regions in the NTE are of particular interest for understanding the involvement of the phytochrome’s NTE in the regulation of its downstream signalling.

Differential phosphorylation of the N‐terminal extension regulates phytochrome B signaling

“…Here, we provide photobiological and physiological evidence that NTE deletion severely enhances thermal reversion of phyB in planta, leading to very low Pfr concentrations even in high light, thus strongly reducing phyB activity (Fig. Deletion of the NTE affected the chromophore and its surrounding hydrogen bonding network, particularly in the Pfr state, which could potentially affect the thermal reversion kinetics, and it was also revealed that the NTE undergoes light-dependent structural changes particularly in the S84-K88 region (Horsten et al, 2016). Until recently there was no structural information about phyB NTE available, as the published crystal structure of Arabidopsis phyB PSM lacks the NTE (Burgie et al, 2014).…”

Structural communication between the chromophore‐binding pocket and the N‐terminal extension in plant phytochrome phyB

“…This interaction is similar for phyB from A. thaliana and S. bicolor, suggesting that it represents a general characteristic of phyB. All other regions in the NTE with HDX rates altered by photoconversion probably lack direct contact with the chromophore itself [8]. It comprises a perturbation of the hydrogen bonding network and the CD portion of the chromophore, reflected by a shift in the conformational Pfr-I/Pfr-II equilibrium.…”

“…The impact of these interactions on the chromophore-binding pocket is small and only observed in the Pfr state. Our packing model for the NTE/PSM interactions suggested that in the Pfr state a stretch with comparably slow intrinsic HDX rates (P28-Q36) may interact with the b1 strand of the GAF domain and its adjacent loop [8] (Fig. Both effects, which most likely constitute the molecular basis for the hypsochromic shift of the electronic absorption in NTE deletion variants (Fig.…”

“…S1) [7,8], are presumably linked although no conclusions can be drawn about possible cause-effect relationships between them. This interaction is similar for phyB from A. thaliana and S. bicolor, suggesting that it represents a general characteristic of phyB.…”

“…In particular, although most prokaryotic phytochromes are light-repressed histidine protein kinases signaling from the C-terminal transmitter module, plant phytochromes are active in the Pfr state, signaling from the PSM directly. Furthermore, recent H/D exchange probed by mass spectrometry (HDX) provided evidence for Pr/Pfr-dependent differences [8]. Moreover, although prokaryotic phytochromes carry an N-terminal extension (NTE) of only about 20 residues, in plant Abbreviations A-B/C-D, C=C stretching of the AB/CD methine bridge; ARR, Arabidopsis response regulator; GAF, cGMP phosphodiesterase/adenylyl cyclase/FhlA; HDX, H/D exchange with mass spectrometry; HOOP, hydrogen-out-of-plane; N-H ip, N-H in-plane bending; NTE, N-terminal extension; PAS, Per/Arnt/Sim; PCB, phycocyanobilin; phyA/B, phytochrome A/B; PHY, phytochrome-specific; PIF, phytochrome interaction factor; Pr/Pfr, red/far-red absorbing form of phytochrome; PSM, photosensory module; PΦB, phytochromobilin; RR, resonance Raman.…”