The TP53RK gene encodes a subunit of the highly conserved 'kinase, endopeptidase, and other proteins of small size' (KEOPS) complex that regulates the second biosynthetic step in the formation of N-6-threonylcarbamoyladenosine (t6A) in the cytosol. T6A is a conserved tRNA modification that occurs at position A37 next to the anticodon stem loop of tRNAs that recognize codons that start with adenosine (ANN codons) and is necessary for translational accuracy and efficiency. Other members of the KEOPS complex include LAGE3 (300060), TPRKB (608680), OSGEP (610107), and GON7 (617436). The KEOPS complex likely has additional functions (summary by Braun et al., 2017).

By cDNA subtraction to identify transcripts expressed by cytolytic-competent cytotoxic T cells but not cytolytic-inactive cytotoxic T cells, followed by PCR of a spleen cDNA library, Abe et al. (2001) cloned TP53RK, which they designated PRPK. The deduced 253-amino acid has a nuclear localization signal and characteristics of a protein kinase, but it lacks some typical protein kinase motifs. PRPK shares 83% amino acid identity with the 244-amino acid mouse protein, with most differences in 9 N-terminal amino acids. Northern blot analysis detected an abundant transcript of about 1.0 kb in testis. Lower expression was found in heart, kidney, and spleen, and no expression was found in the other tissues examined. RT-PCR detected expression in human adherent cancer cell lines of epithelial origin, but not in B-cell lymphoid tumor cell lines. Western blot analysis detected endogenous PRPK in embryonic kidney cells, activated T cells, and a T-cell lymphoma cell line. The apparent molecular mass was 31 kD. Epitope-tagged PRPK localized to the nucleus of transfected COS-7 cells.

Abe et al. (2001) found that recombinant PRPK phosphorylated casein (see 115460) in the presence of Mg(2+), but not Mn(2+). PRPK did not show autophosphorylation activity. PRPK-transfected COS-7 cells showed significant upregulation of p53 (191170) activity, but there was no upregulation of several other transcription factors. PRPK bound p53 in vitro and phosphorylated p53 on ser15 in vitro and in vivo.

By coimmunoprecipitation and in vitro binding assays, Miyoshi et al. (2003) demonstrated that PRPK interacts with CGI-121 (608680). Coprecipitation of p53 with PRPK was inhibited by adding recombinant CGI-121 in vitro, suggesting that CGI-121 may act as an inhibitor of the PRPK-p53 interaction.

Braun et al. (2017) found that TP53RK and the other KEOPS complex proteins LAGE3, OSGEP, and TPRKB localized to both the cytoplasm and the nucleus in human podocyte cell lines. Coimmunoprecipitation studies in HEK293 cells showed that all 4 members of the KEOPS complex interacted with one another and with the DNA-repair protein PARP1 (173870); TP53RK colocalized with PARP1 in renal glomeruli of rat kidney sections. Coimmunoprecipitation studies also showed that TP53RK interacted with proteins of the ATP2/3 complex (see, e.g., 604221) and colocalized with ARP2 and ARP3 at lamellipodia in human podocytes. After shRNA knockdown of TP53RK, the formation of the sublamellar actin network in human podocytes was severely disrupted and podocyte migration was decreased.

By FISH, radiation hybrid analysis, and genomic sequence analysis, Abe et al. (2001) mapped the TP53RK gene to chromosome 20q13.2.

In 4 patients from 3 unrelated families with Galloway-Mowat syndrome-4 (GAMOS4; 617730), Braun et al. (2017) identified homozygous or compound heterozygous mutations in the TP53RK gene (608679.0001-608679.0004). The mutations were found by whole-exome sequencing and high-throughput exon sequencing of gene members of the KEOPS complex after mutations in the OSGEP gene were identified. The mutations were unable to rescue the proliferation defect in human podocytes with shRNA-mediated knockdown of TP53RK, suggesting that the identified human disease alleles impaired protein functionality. Both mutations found in family B77 (608679.0001 and 608679.0002) abrogated the molecular interaction between TP53RK and TPRKB. Knockdown of TP53RK using shRNA in human podocytes resulted in inhibition of nascent protein synthesis, decreased cell proliferation, activation of the unfolded protein response with endoplasmic reticulum (ER) stress and upregulation of the ER-associated proteasomal degradation system, and increased apoptosis associated with activation of the DNA damage response (DDR). Knockdown of TP53RK also disrupted the formation of the sublamellar actin network in human podocytes and decreased podocyte migration. Braun et al. (2017) concluded that TP53RK mutations impair both the canonical and noncanonical functions of the KEOPS complex, resulting in several potential pathogenic mechanisms, including translational attenuation, activation of DDR signaling, increased apoptosis, and defects in actin regulation, which would have major effects on neurons and podocytes. The GAMOS4 families were part of a cohort of 91 GAMOS families who underwent genetic studies: mutations in 3 other genes of the KEOPS complex (LAGE3, OSGEP, and TPRKB) were also identified; mutations in these 4 genes were found in a total of 32 GAMOS families.

Braun et al. (2017) found that CRISPR/Cas9-mediated knockdown of the Tp53rk gene in mouse embryos resulted in smaller head size, with shorter cerebral cortex lengths, cortex-midbrain midline lengths, and cortex widths compared to wildtype embryos, although the differences from controls were not significant.