Alternative titles; symbols
HGNC Approved Gene Symbol: DDX23
Cytogenetic location: 12q13.12 Genomic coordinates (GRCh38): 12:48,829,756-48,852,163 (from NCBI)
Many of the factors involved in the splicing of RNA molecules are conserved in eukaryotes, including the small nuclear ribonuclear particles (snRNPs) U1, U2, U4/U6 and U5, and a number of non-snRNP splicing factors. The snRNPs contain both RNA and protein. During the presplicing reaction, U1 and U2 snRNA are involved in distinguishing intron from exon sequence. U4/U6 and U5 act as a tri-snRNP complex (U4/U6.U5) to align RNA during splice reactions. PRP28 belongs to the DEAD box family of putative ATP-dependent RNA helicases (Teigelkamp et al., 1997).
Using partial peptide sequence data derived by microsequencing 2D gel-purified tri-snRNP proteins, Teigelkamp et al. (1997) isolated a PRP28 (DDX23) cDNA encoding a deduced 821-amino acid, 100-kD polypeptide with an N-terminal RS (arg/ser) domain and a C-terminal domain that contains all of the conserved motifs characteristic of members of the DEAD box family of RNA-stimulated ATPases and RNA helicases. PRP28 shares 37% sequence identity with the S. cerevisiae Prp28 protein, suggesting that it plays an essential function during mammalian pre-mRNA splicing.
Teigelkamp et al. (1997) found that PRP28 can be phosphorylated in vitro by Clk/Sty (CLK1; 601951) and the U1 snRNP-associated kinase (SRPK1; 601939), both of which are known to phosphorylate the RS domains of several splicing factors.
Mathew et al. (2008) demonstrated that SRPK1 copurifies predominantly with the U1 snRNP, whereas SRPK2 (602980) copurifies solely with the tri-snRNP. RNAi-mediated depletion in HeLa cells showed that SRPK2 is essential for cell viability, and that it is required for spliceosomal B complex formation. SRPK2 knockdown resulted in hypophosphorylation of PRP28 and destabilized PRP28 association with the tri-snRNP. Immunodepletion of PRP28 from HeLa cell nuclear extract and complementation studies revealed that PRP28 phosphorylation is required for its stable association with the tri-snRNP and for tri-snRNP integration into the B complex.
By knockdown analysis in U2OS human osteosarcoma cells and HeLa cells, Sridhara et al. (2017) found that SRPK2 was necessary to protect against accumulation of R-loops and to prevent RNA-mediated genomic instability. Similarly, loss of DDX23 triggered genomic instability and was frequent in adenoid cystic carcinoma. Expression of phosphomimetic DDX23 restored genome integrity in SRPK2-depleted cells. Restoration of genome integrity by DDX23 was RNA dependent, as R-loops were the source of DNA damage in DDX23-deficient cells, and restoration required DDX23 RNA helicase activity. DDX23 was directly recruited to chromatin regions containing R-loops, and SPRK2-mediated phosphorylation of DDX23 was required for R-loop suppression.
Using a proteomic screen, Ruan et al. (2019) identified Ddx23 as a double-stranded RNA (dsRNA) sensor that bound to poly(I:C) in amphioxus, an extant basal chordate. Amphioxus Ddx23 preferentially bound short dsRNA molecules, and expression of Ddx23 increased dramatically in response to poly(I:C) stimulation in transfected amphioxus intestine cells. Human and Drosophila DDX23 could also bind poly(I:C), with the N-terminal region of human DDX23 mediating the interaction. Knockdown and overexpression analysis in A549 human lung cancer cells revealed that DDX23 was involved in antiviral responses by binding RNA. Upon poly(I:C) or RNA virus stimulation, human DDX23 translocated from the nucleus to the cytoplasm to interact with TRIF (TICAM1; 607601) or MAVS (609676) through its DExD/H box, thereby triggering antiviral signaling by activating IRF3 (603734) and NFKB (see 164011).
Cryoelectron Microscopy
Charenton et al. (2019) reported cryoelectron microscopy structures of the human pre-B spliceosome complex captured before U1 snRNP (see 180740) dissociation at 3.3-angstrom core resolution and the human U4/U6.U5 tri-snRNP at 2.9-angstrom resolution. U1 snRNP inserts the 5-prime splice site-U1 snRNA helix between the 2 RecA domains of the Prp28 DEAD-box helicase. ATP-dependent closure of the Prp28 RecA domains releases the 5-prime splice site to pair with the nearby U6 ACAGAGA-box sequence presented as a mobile loop. The structures suggested that formation of the 5-prime splice site-ACAGAGA helix triggers remodeling of an intricate protein-RNA network to induce Brr2 helicase relocation to its loading sequence in U4 snRNA, enabling Brr2 to unwind the U4/U6 snRNA duplex to allow U6 snRNA to form the catalytic center of the spliceosome.
Gross (2014) mapped the DDX23 gene to chromosome 12q13.12 based on an alignment of the DDX23 sequence (GenBank BC002366) with the genomic sequence (GRCh37).
Charenton, C., Wilkinson, M. E., Nagai, K. Mechanism of 5-prime splice site transfer for human spliceosome activation. Science 364: 362-367, 2019. [PubMed: 30975767] [Full Text: https://doi.org/10.1126/science.aax3289]
Gross, M. B. Personal Communication. Baltimore, Md. 5/30/2014.
Mathew, R., Hartmuth, K., Mohlmann, S., Urlaub, H., Ficner, R., Luhrmann, R. Phosphorylation of human PRP28 by SRPK2 is required for integration of the U4/U6-U5 tri-snRNP into the spliceosome. Nature Struct. Molec. Biol. 15: 435-443, 2008. [PubMed: 18425142] [Full Text: https://doi.org/10.1038/nsmb.1415]
Ruan, J., Cao, Y., Ling, T., Li, P., Wu, S., Peng, D., Wang, Y., Jia, X., Chen, S., Xu, A., Yuan, S. DDX23, an evolutionary conserved dsRNA sensor, participates in innate antiviral responses by pairing with TRIF or MAVS. Front. Immun. 10: 2202, 2019. [PubMed: 31620127] [Full Text: https://doi.org/10.3389/fimmu.2019.02202]
Sridhara, S. C., Carvalho, S., Grosso, A. R., Gallego-Paez, L. M., Carmo-Fonseca, M., Fernandes de Almeida, S. Transcription dynamics prevent RNA-mediated genomic instability through SRPK2-dependent DDX23 phosphorylation. Cell Rep. 18: 334-343, 2017. [PubMed: 28076779] [Full Text: https://doi.org/10.1016/j.celrep.2016.12.050]
Teigelkamp, S., Mundt, C., Achsel, T., Will, C. L., Luhrmann, R. The human U5 snRNP-specific 100-kD protein is an RS domain-containing, putative RNA helicase with significant homology to the yeast splicing factor Prp38p. RNA 3: 1313-1326, 1997. [PubMed: 9409622]