Structural basis for the Pr-Pfr long-range signaling mechanism of a full-length bacterial phytochrome at the atomic level

Abstract

Light sensing allows organisms to adapt to constantly changing environmental factors. Phytochromes constitute a widespread biological photoreceptor family that typically interconvert between two photostates called Pr (red light-absorbing) and Pfr (far-red light-absorbing). Despite the vast structural information reported on phytochromes, the lack of full-length structures at the (near-)atomic level in both pure Pr and Pfr states leaves gaps in the structural mechanisms involved in the signal transmission pathways during the photoconversion. Here we present three crystallographic structures from the plant pathogen Xanthomonas campestris virulence regulator bacteriophytochrome, including two full-length proteins, in the Pr and Pfr states. The structural findings, combined with mutational, biochemical and computational studies, allow us to describe the signaling mechanism of a full-length bacterial phytochrome at the atomic level, from the isomerization of the chromophore and the β-sheet/α-helix tongue transition to the remodeling of the quaternary assembly of the protein.

Photochemistry and transient intermediates in a bacteriophytochrome photocycle revealed by multiscale simulations

“…The sequence of events that leads to such structural changes however is still not understood, due to the multiple time and space scales involved in the process. 16,20,21,28,29,[32][33][34][35][36][37][38][39][40] Thanks to spectroscopic investigations, we know that the photocycle of bacteriophytochromes involves at least two intermediate states, namely Lumi-R and Meta-R 36,[41][42][43] . The former arises from the photoisomerization; then, on the microsecond time scale, thermal relaxation processes lead to the formation of the Meta-R intermediate.…”

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

“…As another difference, the At phyA map exhibited additional electron density adjacent to the PCM which is accounted for by the NTE. Structural data on full-length bacterial phys indicate that like Dr BphP, these receptors predominantly assemble into head-to-head parallel homodimers ( Gourinchas et al, 2019 ; Takala et al, 2020 ), although other arrangements may be functionally relevant in certain BphPs ( Bellini and Papiz, 2012 ; Otero et al, 2021 ). Taken together, our analysis indicates that At phyA adopts a structure that resembles in key aspects that of the bacterial phytochromes, exemplified by Dr BphP ( Li et al, 2010 ; Björling et al, 2016 ).…”

“…A handful of BphPs were also atomically resolved as intact receptors with associated CTMs ( Bellini and Papiz, 2012 ; Otero et al, 2016 ; Gourinchas et al, 2017 ; Etzl et al, 2018 ). With but few exceptions ( Bellini and Papiz, 2012 ; Otero et al, 2021 ), the full-length BphPs invariably adopted a parallel homodimeric assembly which places the PCM and CTM in tandem, connected via a homodimeric α-helical coiled coil. Although BphP-histidine kinases, as the most frequent BphP class, have to date eluded structural elucidation at atomic resolution, cryo-electron microscopy and solution scattering suggest that they also conform to this principal arrangement ( Li et al, 2010 ; Björling et al, 2016 ).…”