Insight into nuclear body formation of phytochromes through stochastic modelling and experiment

Abstract

Spatial relocalization of proteins is crucial for the correct functioning of living cells. An interesting example of spatial ordering is the light-induced clustering of plant photoreceptor proteins. Upon irradiation by white or red light, the red light-active phytochrome, phytochrome B, enters the nucleus and accumulates in large nuclear bodies (NBs). The underlying physical process of nuclear body formation remains unclear, but phytochrome B is thought to coagulate via a simple protein-protein binding process. We measure, for the first time, the distribution of the number of phytochrome B-containing NBs as well as their volume distribution. We show that the experimental data cannot be explained by a stochastic model of nuclear body formation via simple protein-protein binding processes using physically meaningful parameter values. Rather modelling suggests that the data is consistent with a two step process: a fast nucleation step leading to macroparticles followed by a subsequent slow step in which the macroparticles bind to form the nuclear body. An alternative explanation for the observed nuclear body distribution is that the phytochromes bind to a so far unknown molecular structure. We believe it is likely this result holds more generally for other nuclear body-forming plant photoreceptors and proteins. PAPEROriginal content from this work may be used under the terms of the Creative Commons Attribution 3.0 licence.

Increasing ambient temperature progressively disassembles Arabidopsis phytochrome B from individual photobodies with distinct thermostabilities

“…The structural basis of the light-dependent PB localization of phyB has been extensively investigated. PhyB is a homodimer; PB localization requires the dimeric Pfr form of phyB 40,41,43,46,59 . Each phyB monomer contains an N-terminal photosensory module and a C-terminal output module 20,21 .…”

Out of the Dark and Into the Light: A New View of Phytochrome Photobodies

“…Therefore, they reasoned that photobody formation consists of two steps: a fast nucleation step in which phyB aggregates or binds to other proteins, followed by a slower step of more complex binding. Grima et al (2018) also suggested that photobodies may be hollow, which has since been supported by microscopy evidence (Perrella et al, 2021). In this case, phyB may bind to a structural component, also referred to as a seed component, to initiate formation (Mao et al, 2011;Shevtsov and Dundr, 2011; Figure 2).…”

Membraneless nuclear organelles and the search for phases within phases

“…Once these multivalent molecules reach a local concentration above the threshold level, they assemble into complex polymers and undergo LLPS to promote body formation (Sawyer, Hager, & Dundr, ). Recent modeling of plant phytochrome MLO formation suggests this is a two‐step process, consisting of an initial rapid macroparticle formation step and slow macroparticle aggregation into mature droplets (Grima et al, ). These MLO condensates are structurally stable but their protein and RNA constituents exchange dynamically with the surrounding nucleoplasm.…”