Phytochrome functions as a protein kinase in plant light signalling

Phytochrome functions as a protein kinase in plant light signalling


Phytochromes are red- and far-red-absorbing photoreceptors that regulate plant growth and development in response to environmental light conditions. They exist as dimers with each monomer possessing a covalently linked chromophore, and there are two spectrally distinct red-absorbing Pr and far-red-absorbing Pfr forms. Phytochromes are biosynthesized as the Pr form in the dark, which can be phototransformed into the Pfr form on exposure to red light.

The phototransformation between the two forms induces a highly regulated signalling network for photomorphogenesis, which includes translocation of phytochromes into the nucleus, interaction of phytochromes with a wide array of signalling partners, regulated proteolysis of phytochromes and signalling targets, and transcriptional regulation of various photoresponsive genes. Despite these advances in establishing the phytochrome-mediated light signalling networks in plants, the initial biochemical mechanisms of phytochrome function have not been fully elucidated.

A few decades ago, it was proposed that phytochromes might act as light-regulated protein kinases. This hypothesis was supported by the observation that purified oat phytochrome A (phyA) catalyzed the phosphorylation of serine residues on the photoreceptor itself, that is autophosphorylation.

Subsequently, it was suggested that eukaryotic phytochromes are histidine kinase paralogs with serine/threonine specificity. Moreover, several proteins were reported to be phosphorylated by phytochromes in vitro, such as histone H1, PKS1 (phytochrome kinase substrate 1), cryptochromes, Aux/IAA proteins and FHY1 (far-red elongated hypocotyl 1). While these works suggested that oat phyA is an autophosphorylating serine/threonine kinase, the site of its catalytic activity and the in vivo functional role of this kinase activity remain unknown.

The similarity between phytochromes and prokaryotic protein kinases has long been known Subsequently, a cyanobacterial phytochrome (Cph1) was shown to be a light-regulated histidine kinase, implying that the histidine kinase-related domain (HKRD) in the C-terminal half of plant phytochromes could be responsible for its kinase activity. However, it has been suggested that the HKRD of plant phytochromes is non-functional, because the critical conserved histidine residue for histidine kinase activity is absent and mutating several critical residues required for ATP-binding activity did not qualitatively affect its signalling activity. It is therefore conceivable that the region responsible for the catalytic activity of plant phytochromes resides in domains other than the HKRD.

Recently, phytochromes have been reported to induce rapid in vivo phosphorylation and degradation of PIFs (phytochrome-interacting factors). PIFs are a small subset of basic helix–loop–helix transcription factors that are known to be central players in phytochrome-mediated signalling networks. The physical interaction of phytochromes with PIFs is known to lead to the latter’s phosphorylation, and subsequent degradation via the 26S proteasome. Altogether, these processes permit rapid regulation of gene expression in response to fluctuations in environmental light. Therefore, the phytochrome-induced phosphorylation of downstream signalling components, such as PIFs, may play a direct role to target these and other proteins for proteasome-mediated degradation.

In this study published in Nature Communications, authors first provide evidence that PIFs are phosphorylated by phytochromes in vitro. Then, to investigate the in vivo function of phytochrome kinase activity, they determine the likely kinase domain of Avena sativa phyA (AsphyA) using PIF3 as a substrate and obtain AsphyA mutants displaying reduced kinase activity.

Subsequently, authors demonstrate that transgenic phyA-201 plants expressing AsphyA mutants with reduced kinase activity show reduced photoresponses to far-red light, accompanied by reduced phosphorylation and degradation of PIF3 as compared with transgenic plants expressing wild-type (WT) AsphyA.

Therefore, these results support the hypothesis that phytochromes act as protein kinases in plant light signalling and suggest that phytochrome-mediated phosphorylation participates in the initial steps of phytochrome signalling.