Researchers uncover molecular mechanism of light-induced seed germination in Arabidopsis

A research team led by Prof. Liu Xuncheng from the South China Botanical Garden of the Chinese Academy of Sciences has recently published a study in the journal Plant Communications that sheds new light on the pathways that drive light-induced seed germination in plants. The findings identify a positive regulatory role for the KNOX-type transcription factor BP/KNAT1 in Arabidopsis and delineate its interplay with light-sensing proteins and hormone metabolism.

Seed germination marks the first step in the life cycle of angiosperms, and its precise control is essential for seeds to germinate under optimal environmental conditions. Among external cues, light stands out as a key regulator, detected by specialized photoreceptors including phytochromes, cryptochromes, phototropins, and UVR8. Of these, phytochrome B (phyB)—a receptor for red and far-red light—plays a dominant role in promoting light-triggered germination.

Phytochrome-mediated germination relies on the coordination of light signals with the signaling pathways of abscisic acid (ABA, a germination-inhibiting hormone) and gibberellin (GA, a germination-promoting hormone). The exact molecular mechanisms linking light, phyB, and ABA metabolism have long remained unclear.

To address this gap, the team first pinpointed BP/KNAT1 as a novel component of the light-induced germination pathway. Experiments under “phyB-on” conditions showed that Arabidopsis seeds with mutations in the BP gene exhibited significantly lower germination rates compared to wild-type seeds. Conversely, seeds engineered to overexpress BP displayed markedly higher germination rates after light treatment.

Further genetic analyses revealed that the phyB mutant phyB-9 displayed reduced germination under phyB-on conditions, but overexpression of BP in the phyB-9 background partially rescued the germination phenotype. These results indicate that BP acts genetically downstream of phyB to promote light-dependent seed germination.

To explore how phyB and BP interact at the protein level, the researchers used co-immunoprecipitation and other techniques. They found that BP and phyB physically interact both in vitro and in vivo.

The team then investigated phyB’s impact on BP protein levels in imbibed seeds— a critical stage for germination. They constructed transgenic lines expressing BP in both phyB-deficient and phyB-overexpressing backgrounds. Immunoblot analysis revealed that phyB enhances the stability of BP protein.

Additional experiments—including cell-free degradation assays and treatments with MG132—provided further clarity: under phyB-on conditions, phyB reduces BP’s ubiquitination and thereby prevents its breakdown by the 26S proteasome, allowing BP to accumulate.

Transcriptomic analysis showed that BP suppresses genes involved in ABA biosynthesis and signaling. The team then focused on two ABA biosynthetic genes: NCED6 and NCED9.

Binding assays confirmed that BP directly associates with the NCED6 and NCED9 genes both in vitro and in vivo—an interaction that was weakened in the absence of phyB. Chromatin immunoprecipitation (ChIP) assays further revealed that in bp-9 mutant seeds, levels of H3K27me3—a repressive histone modification that silences gene expression—were significantly lower at the NCED6 and NCED9 loci. This reduction in H3K27me3 correlated with a marked increase in ABA content in the mutant seeds.

This study reveals a key molecular mechanism underlying light-induced seed germination. When Arabidopsis seeds are exposed to red light, activated phyB interacts with BP, stabilizing this transcription factor by reducing its ubiquitination. As BP accumulates, it binds to NCED6 and NCED9, elevating H3K27me3 levels to repress these ABA biosynthetic genes. The resulting decrease in ABA content promotes seed germination, the researchers noted.