Disordered protein interactions for an ordered cellular transition: Cdc2-like kinase 1 is transported to the nucleus via its Ser–Arg protein substrate

Abstract

Edited by Karin Musier-Forsyth Serine-arginine (SR) proteins are essential splicing factors that promote numerous steps associated with mRNA processing and whose biological function is tightly regulated through multi-site phosphorylation. In the nucleus, the cdc2-like kinases (CLKs) phosphorylate SR proteins on their intrinsically disordered Arg-Ser (RS) domains, mobilizing them from storage speckles to the splicing machinery. The CLKs have disordered N termini that bind tightly to RS domains, enhancing SR protein phosphorylation. The N termini also promote nuclear localization of CLKs, but their transport mechanism is presently unknown. To explore cytoplasmic-nuclear transitions, several classical nuclear localization sequences in the N terminus of the CLK1 isoform were identified, but their mutation had no effect on subcellular localization. Rather, we found that CLK1 amplifies its presence in the nucleus by forming a stable complex with the SR protein substrate and appropriating its NLS for transport. These findings indicate that, along with their well-established roles in mRNA splicing, SR proteins use disordered protein-protein interactions to carry their kinase regulator from the cytoplasm to the nucleus.

Cdc-Like Kinases (CLKs): Biology, Chemical Probes, and Therapeutic Potential

“…On the other hand, NLS strongly interacts with its substrate SRSF1 (SR protein), which is very likely important for the nuclear import of CLK1 via a “piggyback” mechanism, where CLK1 is transported inside the nucleus together with the TRN-SR2/SRSF1 complex ( Figure 6 ). This mechanism has been supported by various experiments, for example, disruption of SRSF1 protein transport by TRN-SR2 knockdown or mutation of the SRSF1 NLS impaired CLK1 nuclear localization [ 68 ].…”

“…For instance, CLK1 expression level in the testes was significantly lower than those of CLK2-4 [ 53 , 65 , 66 , 67 ]. All CLK isoforms are mostly localized in the nucleus; however, in the testes, CLK3 was found to be localized mostly in stress granules in the cytoplasm [ 16 , 52 , 68 ]. In contrast, SRPKs were found mostly in the cytoplasm and only a minor fraction was observed in the nucleus [ 69 , 70 ].…”

“…The spliced variants form heterodimers with full-length CLKs, showing that alternative splicing mediated by CLKs is auto-regulated [ 69 ]. CLKs are mostly localized in the nucleus, but their localization has been described also in the cytoplasm (e.g., in stress granules) [ 16 , 52 , 68 ], although less abundantly than SRPKs [ 69 , 70 ].…”

“…Not only nuclear import but also nuclear function has been described most thoroughly for the CLK1 isoform, namely its regulation mechanism of the SR protein SRSF1 [ 55 , 68 , 85 , 86 ]. In this process, CLK1 and SRPK1 work co-operatively as a complex [ 55 ].…”

“… Schematic representation of the phosphorylation mechanism involving CLK1 [ 39 , 49 , 55 , 68 , 82 , 83 , 84 , 85 ]. …”