phyB photobodies display molecular memory, regulating light signaling transcriptional states through phase separation.

Abstract

Phytochrome B is a crucial red and far-red light sensor, which controls plant development and environmental responses to light and temperature. In the nucleus, phyB forms phase separated condensates, also called photobodies, consisting of various transcriptional regulators and transcription factors. phyB photobodies can form or disperse depending on the amount of light, the light quality, or ambient temperature. However, the biological relevance for forming photobodies is still unclear. In recent years the study of condensates has given rise to the idea that condensates can act as molecular memory, either due to long equilibration timescales arising from strong interactions can kinetically trap a mixture in a phase-separated state beyond the equilibrium coexistence line, or from phase-separation dependent modification processes or transcriptional regulation. Here, we hypothesize that the formation of phyB photobodies and the associated sequestration of signaling molecules allows for the formation of cell-type specific memory about light conditions. To address this hypothesis, we first developed a live imaging setup of phyB photobodies which shows that they do not follow classic liquid-liquid phase separation dynamics, but instead have a restriction on their size, intensity and minimum number. Fluorescence recovery after photobleaching (FRAP) then showed that photobodies between cell types have different levels of mobilities and diffusivities, suggesting that they are more stable in darkness or high red light, versus low red light. These differences in phyB photobody stability between cell types were also confirmed through whole-mount confocal imaging and single-nucleus transcriptomics in the same light-perturbation series. Through sci-Seq single nucleus spatial transcriptomics of the cotyledon in this light perturbation series, we identify a photobody-associated transcriptional cluster of nuclei that regulates photosynthesis, circadian rhythm, and RNA processing; the phyB photobody likely promotes its own stability by regulating TZP and PCH1 expression. The correlation between photobodies and transcriptional regulation shows how phyB condensates can provide cell-type specific light responses and exhibit signaling memory in changing environmental conditions.