Kinase Family CDKL

Kinase Classification: Group CMGC: Family CDKL

The CDKL (CDK-Like) family is very similar to CDK but are not known to interact with cyclins, and are distinct from CDKs and found in all eukaryotes other than fungi. Little is known of their function. Humans have 5 CDKLs (CDKL1-5), of which 1-4 are similar and 5 is distinctive in evolution and sequence.

Evolution

CDKL kinases are found in all eukaryotes examined to date other than fungi. CDKL1 and CDKL2 are similar and probably derive from an early vertebrate duplication; CDKL3 and CDKL4 are recent inventions, and are absent from fish; while CDKL5 has specific orthologs all the way back to early protist, but is absent from major models like Drosophila and C. elegans.

Domain Structure

CDKLs generally have a N-terminal kinase domain followed by a divergent sequence of up to several hundred AA without any other known domains.

Unlike their closest relatives, CDKs, all CDKL have TxY motif in their activation loop, like MAPK and RCK families. Phosphosite shows that the TxY tyrosine of CDKL5 is highly phosphorylated. Y262 is also heavily phosphorylated. It is conserved in CDKL5 homologs even in ciliates, but not in other CDKL. Phosphosite has no data for CDKL2-4. CDKL5 autophosphorylates on the TxY motif, as assayed by a cross-reacting anti-MAPK antibody; it's not clear which of the TxY residues are phosphorylated in this assay [1]. All CDKL also conserve the Y in the G-rich loop that is the Wee1 site equivalent in CDK1, but it has not been reported as phosphorylated.

Function

CDKL1 associates with TGFb pathway proteins TGFbR1 and SMURF1 in a targeted protein interaction screen [2], and may correlate with Drosophila CDKL being found in a TGFb pathway RNAi screen [3]. It is expressed selectively in glial cells of the brain [4], and was weakly associated with cognitive behavior in a GWAS study [5]. Zebrafish CDKL1 is expressed from fertilization onwards, and is particularly high in ovary, testis, and brain, and knockdown lead to brain and eye malformation, pericardial edema, and body axis curvature [6].

CDKL1 and CDKL2 were expressed in opposing reproductive tissues: Ovary for CDKL1 and Testis for CDKL2, and both were enzymatically activated by EGF stimulation, though this did not require TxY activation loop phosphorylation [7]. CDKL2 is expressed in various sets of brain neurons in mice [8][9] and expression is induced in rabbit brains during a learning test [10] and knockout mice also suggested a role in cognitive function [11]. Re-analysis of a breast cancer GWAS study also highlighted CDKL2, along with EPH receptors, as possible contributors to cancer [12].

CDKL3 is also expressed in CNS neurons, in a developmentally-regulated pattern [13]. Knockdown and overexpression in cultured cells suggested that it functions to increase dendrite growth and branching and to inhibit axonal growth. CDKL3 was linked to one case of mild mental retardation in which a translocation breakpoint was mapped to within CDKL3, resulting in a halving of expression level [14]. A kinome RNAi screen identified CDKL3 as a one of 9 suppressors of microautophagy [15], while overexpression of CDKL3 in cell lines resulted in increased proliferation [16].

CDKL4 has never been characterized. The human form contains a single AA change at a conserved arginine that is likely to reduce or eliminate kinase activity (this AA is conserved across all other CDKL) (Reuben Valas, Gerard Manning, unpublished).

The C. elegans CDKL5, Y42A5A.4, is not functionally annotated, but Drosophila CG7236 has a wealth of high-throughput data. RNAi knockdown in S2 and Kc cells show that knockdown induces multinucleate cells [17][18][19], a decreased mitotic index [17], and large cells or large nuclei [20]. In a screen of 3 hemocyte lines (S2, S2R+ and Kc), and three neuronal cells, CG7236 was expressed in all cells but had a phenotype only in the hemocyte lines.

In protein interaction screens, it shows an interaction with Cyclin K, suggesting that it might indeed be a cyclin-interacting class of kinases. In another RNAi screen, CG72336 caused a phenotype of large cells, large nuclei and multinucleate cells in 3 hemocyte cell lines (S2, S2R+ and Kc), but no phenotype in a trio of neuronal cell lines, despite being expressed in all cells [20]. CG72336 also emerged as one of 701 genes in a screen for JNK signaling [21], and as one of 346 genes that disrupted TGFb (dpp) signaling [3].

In Trypanosoma brucei, mutants the CDKL TbECK1 is expressed constitutively throughout the lifecycle and a truncation of the C-terminal tail induces a slow-growth phenotype [22]

References

1. Bertani I, Rusconi L, Bolognese F, Forlani G, Conca B, De Monte L, Badaracco G, Landsberger N, and Kilstrup-Nielsen C. Functional consequences of mutations in CDKL5, an X-linked gene involved in infantile spasms and mental retardation. J Biol Chem. 2006 Oct 20;281(42):32048-56. DOI:10.1074/jbc.M606325200 |
2. Barrios-Rodiles M, Brown KR, Ozdamar B, Bose R, Liu Z, Donovan RS, Shinjo F, Liu Y, Dembowy J, Taylor IW, Luga V, Przulj N, Robinson M, Suzuki H, Hayashizaki Y, Jurisica I, and Wrana JL. High-throughput mapping of a dynamic signaling network in mammalian cells. Science. 2005 Mar 11;307(5715):1621-5. DOI:10.1126/science.1105776 |
3. Xu L, Yao X, Chen X, Lu P, Zhang B, and Ip YT. Msk is required for nuclear import of TGF-{beta}/BMP-activated Smads. J Cell Biol. 2007 Sep 10;178(6):981-94. DOI:10.1083/jcb.200703106 |
4. Yen SH, Kenessey A, Lee SC, and Dickson DW. The distribution and biochemical properties of a Cdc2-related kinase, KKIALRE, in normal and Alzheimer brains. J Neurochem. 1995 Dec;65(6):2577-84. DOI:10.1046/j.1471-4159.1995.65062577.x |
5. Cirulli ET, Kasperaviciūte D, Attix DK, Need AC, Ge D, Gibson G, and Goldstein DB. Common genetic variation and performance on standardized cognitive tests. Eur J Hum Genet. 2010 Jul;18(7):815-20. DOI:10.1038/ejhg.2010.2 |
6. Hsu LS, Liang CJ, Tseng CY, Yeh CW, and Tsai JN. Zebrafish cyclin-dependent protein kinase-like 1 (zcdkl1): identification and functional characterization. Int J Mol Sci. 2011;12(6):3606-17. DOI:10.3390/ijms12063606 |
7. Taglienti CA, Wysk M, and Davis RJ. Molecular cloning of the epidermal growth factor-stimulated protein kinase p56 KKIAMRE. Oncogene. 1996 Dec 19;13(12):2563-74.
8. Sassa T, Gomi H, Sun W, Ikeda T, Thompson RF, and Itohara S. Identification of variants and dual promoters of murine serine/threonine kinase KKIAMRE. J Neurochem. 2000 May;74(5):1809-19. DOI:10.1046/j.1471-4159.2000.0741809.x |
9. Sassa T, Gomi H, and Itohara S. Postnatal expression of Cdkl2 in mouse brain revealed by LacZ inserted into the Cdkl2 locus. Cell Tissue Res. 2004 Feb;315(2):147-56. DOI:10.1007/s00441-003-0828-8 |
10. Gomi H, Sun W, Finch CE, Itohara S, Yoshimi K, and Thompson RF. Learning induces a CDC2-related protein kinase, KKIAMRE. J Neurosci. 1999 Nov 1;19(21):9530-7. DOI:10.1523/JNEUROSCI.19-21-09530.1999 |
11. Gomi H, Sassa T, Thompson RF, and Itohara S. Involvement of cyclin-dependent kinase-like 2 in cognitive function required for contextual and spatial learning in mice. Front Behav Neurosci. 2010;4:17. DOI:10.3389/fnbeh.2010.00017 |
13. Liu Z, Xu D, Zhao Y, and Zheng J. Non-syndromic mild mental retardation candidate gene CDKL3 regulates neuronal morphogenesis. Neurobiol Dis. 2010 Sep;39(3):242-51. DOI:10.1016/j.nbd.2010.03.015 |
14. Dubos A, Pannetier S, and Hanauer A. Inactivation of the CDKL3 gene at 5q31.1 by a balanced t(X;5) translocation associated with nonspecific mild mental retardation. Am J Med Genet A. 2008 May 15;146A(10):1267-79. DOI:10.1002/ajmg.a.32274 |
15. Szyniarowski P, Corcelle-Termeau E, Farkas T, Høyer-Hansen M, Nylandsted J, Kallunki T, and Jäättelä M. A comprehensive siRNA screen for kinases that suppress macroautophagy in optimal growth conditions. Autophagy. 2011 Aug;7(8):892-903. DOI:10.4161/auto.7.8.15770 |
16. Jaluria P, Betenbaugh M, Konstantopoulos K, and Shiloach J. Enhancement of cell proliferation in various mammalian cell lines by gene insertion of a cyclin-dependent kinase homolog. BMC Biotechnol. 2007 Oct 18;7:71. DOI:10.1186/1472-6750-7-71 |
17. Bettencourt-Dias M, Giet R, Sinka R, Mazumdar A, Lock WG, Balloux F, Zafiropoulos PJ, Yamaguchi S, Winter S, Carthew RW, Cooper M, Jones D, Frenz L, and Glover DM. Genome-wide survey of protein kinases required for cell cycle progression. Nature. 2004 Dec 23;432(7020):980-7. DOI:10.1038/nature03160 |
18. Kiger AA, Baum B, Jones S, Jones MR, Coulson A, Echeverri C, and Perrimon N. A functional genomic analysis of cell morphology using RNA interference. J Biol. 2003;2(4):27. DOI:10.1186/1475-4924-2-27 |
19. Echard A, Hickson GR, Foley E, and O'Farrell PH. Terminal cytokinesis events uncovered after an RNAi screen. Curr Biol. 2004 Sep 21;14(18):1685-93. DOI:10.1016/j.cub.2004.08.063 |
20. Liu T, Sims D, and Baum B. Parallel RNAi screens across different cell lines identify generic and cell type-specific regulators of actin organization and cell morphology. Genome Biol. 2009;10(3):R26. DOI:10.1186/gb-2009-10-3-r26 |
21. Bond D and Foley E. A quantitative RNAi screen for JNK modifiers identifies Pvr as a novel regulator of Drosophila immune signaling. PLoS Pathog. 2009 Nov;5(11):e1000655. DOI:10.1371/journal.ppat.1000655 |
22. Ellis J, Sarkar M, Hendriks E, and Matthews K. A novel ERK-like, CRK-like protein kinase that modulates growth in Trypanosoma brucei via an autoregulatory C-terminal extension. Mol Microbiol. 2004 Sep;53(5):1487-99. DOI:10.1111/j.1365-2958.2004.04218.x |
23. Bonifaci N, Górski B, Masojć B, Wokołorczyk D, Jakubowska A, Dębniak T, Berenguer A, Serra Musach J, Brunet J, Dopazo J, Narod SA, Lubiński J, Lázaro C, Cybulski C, and Pujana MA. Exploring the link between germline and somatic genetic alterations in breast carcinogenesis. PLoS One. 2010 Nov 22;5(11):e14078. DOI:10.1371/journal.pone.0014078 |