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Proximity proteomics reveals the molecular architecture of phytochrome B photobodies in Arabidopsis thaliana

Kate Olson,Jae-Hyung Lee,M. Dean,Thu Minh Doan,Allison M. Manuel,Chan Yul Yoo

Published 2025 in bioRxiv

ABSTRACT

The red/far-red light photoreceptor phytochrome B (phyB) forms light-induced subnuclear condensates, termed photobodies, that coordinate plant responses to light and temperature. Despite their central role in environmental signaling, the molecular composition of phyB photobodies during their early formation has remained unknown. Here, we established an in planta proximity labeling approach using miniTurbo-based biotinylation in Arabidopsis thaliana to capture proteins associated with phyB photobodies during early de-etiolation. Mass spectrometry identified 42 high-confidence proximal proteins, including 11 known core components and 31 previously unrecognized photobody-associated proteins. Among these, the co-chaperone HOP1 forms light-dependent nuclear condensates that partially co-localize with phyB photobodies. HOP1 condensates are smaller in the wild-type background than in phyB-overexpressing seedlings, and HOP1 overexpression enhanced cotyledon expansion under red light. These findings suggest that HOP1 contributes to photomorphogenesis by stabilizing phyB photobodies and sustaining active phyB signaling. Together, our results reveal that nascent large phyB photobodies function as dynamic hubs integrating chaperone-mediated protein quality control with transcriptional regulation, providing the first in planta proteomic framework for understanding photobody assembly and signaling in plants.

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