Scientists Discover Photoreceptor phyB Stabilizes the KNOX Transcription Factor BP/KNAT1 to Promote Light-induced Seed Germination

Recently, the team led by Professor LIU Xuncheng at the South China Botanical Garden, Chinese Academy of Sciences, published a research article titled “Phytochrome B stabilizes the KNOX transcription factor BP/KNAT1 to promote light-initiated seed germination in Arabidopsis thaliana”in the plant science journal Plant Communications.The study elucidates that the KNOX-type transcription factor BP/KNAT1 in Arabidopsis acts as a positive regulator of light-induced seed germination. The red/far-red light photoreceptor phytochrome B (phyB) directly interacts with BP and promotes its accumulation in imbibed seeds by reducing its ubiquitination level. BP, in turn, directly represses the expression of ABA biosynthetic genes NCED6 and NCED9 by increasing the levels of the repressive histone modification H3K27me3, thereby decreasing ABA content and promoting seed germination. This work not only identifies a new component in the light-induced seed germination pathway but also deepens this understanding of the regulatory mechanism by which phyB promotes light-dependent seed germination.

Seed germination is the first step in the growth of angiosperms, and its precise regulation is crucial for selecting suitable conditions for seed development. Among various external environmental factors, light is considered one of the key regulators of seed germination and is perceived by multiple photoreceptors, including phytochromes, cryptochromes, phototropins, and UVR8. Phytochromes are red/far-red (R/FR) light receptors, with phytochrome B (phyB) playing a dominant role in promoting light-induced seed germination. Phytochrome-mediated seed germination mainly relies on the coordination of light signals with abscisic acid (ABA) and gibberellin (GA) signaling. However, the precise mechanisms by which light, phyB, and ABA metabolism regulate seed germination remain largely unclear.

The research team identified the KNOX-type transcription factor BP/KNAT1 in Arabidopsis as a new component in the light-induced seed germination pathway. Under phyB-on conditions, BP mutants exhibited significantly lower germination rates compared to wild type, whereas BP-overexpressing seeds showed markedly increased germination rates after 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.

The genetic interaction between phyB and BP prompted the researchers to investigate whether they interact at the protein level. Co-immunoprecipitation and other assays demonstrated that BP physically interacts with phyB both in vitro and in vivo. To further examine the effect of phyB on BP protein levels in imbibed seeds, transgenic lines expressing BP were constructed in both phyB-deficient and phyB-overexpressing backgrounds. Immunoblot analysis revealed that the presence of phyB enhanced BP protein stability. Cell-freedegradation assays and MG132 treatment experiments indicated that phyB may promote the accumulation of BP by decreasing its ubiquitination and 26S proteasome-mediated degradation in the phyB-on condition.

Transcriptomic analysis indicated that BP represses ABA biosynthesis and signaling pathways. Binding assays demonstrated that BP directly associates with NCED6/9 both in vitro and in vivo, and the absence of phyB reduces this interaction. ChIP assays and ABA measurements revealed that in the bp-9 mutant seeds, the H3K27me3 levels at NCED6/9 were significantly decreased, whereas ABA content was markedly increased. These results indicate that BP directly binds to NCED6/9 and represses ABA biosynthesis by elevating H3K27me3 modification levels.

In summary, the research team revealed the core molecular mechanism of the phyB-BP-NCED6/9 regulatory module in light-initiated seed germination:Upon exposure to R light, activated phyB interacts with and stabilizes BP by removing its ubiquitination. The accumulated BP binds to and represses NCED6/9 expression by increasing the levels of H3K27me3, leading to a decreased ABA level thereby initiating seed germination. Paper link: https://www.cell.com/plant-communications/fulltext/S2590-3462(25)00279-2

Figure 1. Proposed working model of the phyB-BP-NCED6/9 cascade in light-initiated seed germination.(image by ZHANG et al)