Cryo-Electron Microscopy of Arabidopsis thaliana Phytochrome A in Its Pr State Reveals Head-to-Head Homodimeric Architecture

Abstract

Phytochrome photoreceptors regulate vital adaptations of plant development, growth, and physiology depending on the ratio of red and far-red light. The light-triggered Z/E isomerization of a covalently bound bilin chromophore underlies phytochrome photoconversion between the red-absorbing Pr and far-red-absorbing Pfr states. Compared to bacterial phytochromes, the molecular mechanisms of signal propagation to the C-terminal module and its regulation are little understood in plant phytochromes, not least owing to a dearth of structural information. To address this deficit, we studied the Arabidopsis thaliana phytochrome A (AtphyA) at full length by cryo-electron microscopy (cryo-EM). Following heterologous expression in Escherichia coli, we optimized the solvent conditions to overcome protein aggregation and thus obtained photochemically active, near-homogenous AtphyA. We prepared grids for cryo-EM analysis of AtphyA in its Pr state and conducted single-particle analysis. The resulting two-dimensional class averages and the three-dimensional electron density map at 17 Å showed a homodimeric head-to-head assembly of AtphyA. Docking of domain structures into the electron density revealed a separation of the AtphyA homodimer at the junction of its photosensor and effector modules, as reflected in a large void in the middle of map. The overall architecture of AtphyA resembled that of bacterial phytochromes, thus hinting at commonalities in signal transduction and mechanism between these receptors. Our work paves the way toward future studies of the structure, light response, and interactions of full-length phytochromes by cryo-EM.

Phytochrome phosphorylation in plant light signaling

“…Phytochromes are dimers, and each monomer comprises an N-terminal photosensory module (PSM) and a C-terminal output module (OPM) connected by a hinge region ( Figure 2A ). In the PSM, a PAS-GAF-PHY tri-domain, also known as the photosensory core for absorbing light, is responsible for the bilin lyase activity of phytochromes to bind a tetrapyrrole chromophore to a conserved cysteine residue ( Wahlgren et al., 2021 ; Li et al., 2022 ). In addition, an N-terminal extension (NTE; 1–65 aa region of AsphyA) has been reported to be essential for biological activity ( Cherry et al., 1992 ).…”

The Red Edge: Bilin-Binding Photoreceptors as Optogenetic Tools and Fluorescence Reporters

“…The crystallization-based structural information obtained from various phytochromes was recently complemented by a full-length cryo-EM-based structure of At PhyA. 134 The electron microscopy experiments yielded an electron density with a resolution of 17 Å and combined with docking of domains from crystallization studies allowed to propose the positions of the two plant-Phy specific PAS domains (named PAS-A and PAS-B) located between the PHY domain and the C-terminal part of the protein.…”