New interaction partners for Nek4.1 and Nek4.2 isoforms: from the DNA damage response to RNA splicing

Abstract

BackgroundNeks are serine-threonine kinases that are similar to NIMA, a protein found in Aspergillus nidulans which is essential for cell division. In humans there are eleven Neks which are involved in different biological functions besides the cell cycle control. Nek4 is one of the largest members of the Nek family and has been related to the primary cilia formation and in DNA damage response. However, its substrates and interaction partners are still unknown. In an attempt to better understand the role of Nek4, we performed an interactomics study to find new biological processes in which Nek4 is involved. We also described a novel Nek4 isoform which lacks a region of 46 amino acids derived from an insertion of an Alu sequence and showed the interactomics profile of these two Nek4 proteins.Results and discussionIsoform 1 and isoform 2 of Nek4 were expressed in human cells and after an immunoprecipitation followed by mass spectrometry, 474 interacting proteins were identified for isoform 1 and 149 for isoform 2 of Nek4. About 68% of isoform 2 potential interactors (102 proteins) are common between the two Nek4 isoforms. Our results reinforce Nek4 involvement in the DNA damage response, cilia maintenance and microtubule stabilization, and raise the possibility of new functional contexts, including apoptosis signaling, stress response, translation, protein quality control and, most intriguingly, RNA splicing. We show for the first time an unexpected difference between both Nek4 isoforms in RNA splicing control. Among the interacting partners, we found important proteins such as ANT3, Whirlin, PCNA, 14-3-3ε, SRSF1, SRSF2, SRPK1 and hNRNPs proteins.ConclusionsThis study provides new insights into Nek4 functions, identifying new interaction partners and further suggests an interesting difference between isoform 1 and isoform 2 of this kinase. Nek4 isoform 1 may have similar roles compared to other Neks and these roles are not all preserved in isoform 2. Besides, in some processes, both isoforms showed opposite effects, indicating a possible fine controlled regulation.Electronic supplementary materialThe online version of this article (doi:10.1186/s12953-015-0065-6) contains supplementary material, which is available to authorized users.

Targeting the TLK1/NEK1 DDR axis with Thioridazine suppresses outgrowth of androgen independent prostate tumors

“…For example Nek2 is critical for centrosome duplication, whereas Nek6, 7, 9 are regulators of the mitotic spindle and cytokinesis . Nek1 and Nek4 have been linked to the DDR and DNA repair pathways. Nek1 promotes Chk1 activation via its association with ATR‐ATRIP and primes ATR for the DDR .…”

Checking NEKs: Overcoming a Bottleneck in Human Diseases

“…The clear function and involvement of NEK4 in cellular processes are yet to be determined, but it is suggested that NEK4 participates in primary cilium assembly, regulation of microtubule stabilization [25], the DNA damage response (DDR) [31], and RNA splicing [18]. A second functional isoform [18], which is similar to the murine NEK4 long isoform and named NEK4.2, has been identified in humans, and different interactors to NEK4.1 have been described. Given the potential involvement of NEK4 in ciliary function and the DNA damage response, the association with human disorders is to be expected.…”

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“…For example NEK2 is critical for centrosome duplication, 11 whereas NEK6, 7, 9 are regulators of the mitotic spindle and cytokinesis. 25 NEK1, 9,10,26 and NEK4 27 have been linked to the DDR and DNA repair pathways. NEK1 mediates Chk1 activation via an unclear mechanism since 2 papers reported opposite results using siRNA depletion experiments.…”