Arabidopsis inositol polyphosphate kinases regulate COP9 signalosome functions in phosphate-homeostasis

Plant Cullin RING Ubiquitin E3 ligases (CRLs) facilitate targeted protein degradation during physiological development and adaptation to stress. The deneddylase activity of COP9 signalosome (CSN) regulates cellular ratios of neddylated cullins available for the continuum of CRL functions. While selective inositol polyphosphates (InsPs) function as co-factors in plant responses involving the ubiquitylation of negative regulators, a relationship to CSN-CRL activities has not yet been established. Here, we show that the two Arabidopsis thaliana InsP-kinases IPK1 and ITPK1 physically interact and metabolically connect with the CSN holo-complex to modulate cullin deneddylation efficiency. Specifically, functional deficiency of ITPK1 lowers cullin deneddylation rates and disrupts the dissociation equilibrium of CSN5, the deneddylase catalytic subunit, and CUL1 with the holo-complex. Our results identify a novel auto-regulatory switch of CSN functions, defined by deneddylation activity. We further demonstrate that phosphate starvation response (PSR), which is induced in Pi-starved wild-type plants and constitutive in the above InsP-kinase mutants, is orchestrated in part by reduced deneddylation rates that, in turn, affect the stability of SPX4, a key negative regulator of PSR. Pharmacological inhibition of cullin neddylation stabilizes SPX4 and impairs PSR, thus linking CSN-CRL dynamics to phosphate (Pi)-sensing. Conversely, when exposed to compounds that inhibit CSN5 deneddylase activity, wild-type plants display phenotypes similar to the above InsP-kinase mutants. Overall, our data reveal that the regulation of plant Pi-starvation responses by specific InsP-kinases is caused by a direct role of these kinases in balancing coordination between CRL-CSN activities.