DEAD-box RNA Helicases Act as Nucleotide Exchange Factors for Casein Kinase 2

Abstract

DDX RNA helicases promote RNA processing but DDX3X is also known to activate casein kinase 1 ϵ (CK1ϵ). Here we show that not only is protein kinase stimulation a latent property of other DDX proteins towards CK1ϵ, but that this extends to casein kinase 2 (CK2α2) as well. CK2α2 enzymatic activity is stimulated by a variety of DDX proteins and we identify DDX1/24/41/54 as physiological activators required for full kinase activity in vitro and in Xenopus embryos. Mutational analysis of DDX3X reveals that CK1 and CK2 kinase stimulation engages its RNA binding- but not catalytic motifs. Mathematical modelling of enzyme kinetics and stopped-flow spectroscopy converge that DDX proteins function as nucleotide exchange factor towards CK2α2 that reduce unproductive reaction intermediates and substrate inhibition. Our study reveals protein kinase stimulation by nucleotide exchange as a new principle in kinase regulation and an evolved function of DDX proteins.

Amplicon structure creates collateral therapeutic vulnerability in cancer

“…It also needs to be tested if DDX1 interacts with DLST at physiological protein levels in untransformed cells, or if this only occurs in the context of aberrant DDX1 expression in DDX1-MYCN- amplified cancer cells. Since the ATPase activity of DDX proteins are required for their role in DNA and RNA biology, it is conceivable that these functions are not required for DDX1 to establish stable interactions with protein substrates such as a-α-KGDH or as recently reported with casein kinase 2 (Fatti et al, 2021). Whether such canonical DDX1 functions also influence mitochondrial metabolism and thereby contribute to the observed mTORC1 dependency remains to be investigated.…”

Substrate Specificities of DDX1: A Human DEAD-box protein

“…The human DDX1 protein is a member of the DEAD-box enzyme family, which engages in a wide range of cellular processes, including DNA double-strand break repair, RNA transcription, ribosomal RNA (rRNA), microRNA (miRNA) and transfer RNA (tRNA) processing, messenger RNA (mRNA) 3' end maturation, translation initiation, and RNA transport, storage, and decay [2][3][4][5][6][7][8][9][10][11][12][13] . Consequently, this protein is implicated in the progressions of cancers, viral infections, and embryonic development 3,[14][15][16][17][18][19] . Here we examine the identity of the nucleotides that the DDX1 protein hydrolyzes and the properties of the structures and sequences of the nucleic acid substrates that support the DDX1 protein's ATPase activity.…”