Phytochrome B sets condensate number through graded nucleator states and seeding-site efficacy

Abstract

Abstract Photobodies (PBs) are phytochrome B (phyB)-organized nuclear condensates that nucleate at defined subnuclear seeding sites and decrease in number with warming. How cells set PB number—and, more broadly, condensate number—remains poorly understood. Here we show that phyB’s output module (OPM) functions as a universal nucleator for all site-defined PB types, whereas the photosensory module (PSM) attenuates this activity, enabling environmental control. Consistently, missense substitutions in OPM genetically separate intrinsic nucleation potency from PSM-mediated regulation. Unexpectedly, the constitutively active phyB Y276H allele defines a hypoactive nucleation state, supporting graded active conformations with distinct nucleation potency. Temperature tunes PB number through two separable inputs—phyB thermal reversion (nucleator state) and temperature-responsive seeding-site efficacy—whose contributions vary across sites and cell types. Together, these results distinguish nucleation control (number) from growth control (size) and show that condensate number is jointly determined by nucleator state and seeding-site efficacy.