Alternative titles; symbols
HGNC Approved Gene Symbol: SDE2
Cytogenetic location: 1q42.12 Genomic coordinates (GRCh38): 1:225,982,702-225,999,343 (from NCBI)
SDE2 is proteolytically cleaved to release an N-terminal ubiquitin-like (UBL) fragment and a functional C-terminal fragment (Jo et al., 2016). The SDE2 C-terminal fragment binds RNA and is involved in pre-mRNA splicing (Thakran et al., 2018) and rRNA processing and ribosome biogenesis (Floro et al., 2021). The SDE2 C-terminal fragment also binds DNA and is involved in protection of DNA replication forks in response to replication stress (Rageul et al., 2020; Weinheimer et al., 2022).
Sugioka-Sugiyama and Sugiyama (2011) identified yeast Sde2, which encodes a predicted 263-amino acid protein with orthologs present in various eukaryotic species, including human and mouse. The N- and the C-terminal regions of Sde2 are highly conserved. Fluorescent microscopic assays showed that Sde2 with a C-terminal localized to nucleus in yeast.
Jo et al. (2016) stated that human SDE2 contains 451 amino acids and has a 77-amino acid N-terminal UBL domain and a C-terminal SDE domain. The UBL domain contains a conserved diglycine motif for cleavage at its C-terminal end.
Rageul et al. (2020) noted that the functional C-terminal fragment of human SDE2 contains a conserved SDE2 domain and a SAP domain.
By cellular fractionation, Floro et al. (2021) showed that SDE2 distributed across both the nucleus and cytoplasm in human cells.
Weinheimer et al. (2022) noted that human SDE2 protein contains a UBL domain, a coiled-coil SDE2 domain, and a SAP domain. The predicted SAP domain exhibits a bipartite distribution of hydrophobic and polar residues, separated by a linker loop containing a glycine residue.
Gross (2024) mapped the SDE2 gene to chromosome 1q42.12 based on an alignment of the SDE2 sequence (GenBank BC071563) with the genomic sequence (GRCh38).
By knockout analysis, Sugioka-Sugiyama and Sugiyama (2011) showed that Sde2 was required for telomeric silencing in yeast. Sde2 was also essential for normal cell growth, was involved in the DNA damage response and DNA repair, and contributed to chromosome stability in mitotic yeast cells. Sde2 genetically interacted with factors involved in telomere function and/or maintenance of functional telomeres. Sde2 also participated in recruitment of the silencing complex SHREC, which in turn prevented transcription at telomeres by Pol II (see 180660).
Using GFP-tagged recombinant protein expressed in HeLa cells, Jo et al. (2016) showed that SDE2 was cleaved at its diglycine motif by deubiquitinating (DUB) enzyme to release the UBL. The UBL contains a conserved PIP box, through which SDE2 interacted with PCNA (176740), and interaction with PCNA was required for cleavage of SDE2. Upon cleavage, both the N-terminal UBL and C-terminal fragment of SDE2 were degraded via CRL4 (see 600045)-CDT2 (DTL; 610617)-mediated proteolysis. SDE2 cleavage and subsequent degradation was a normal turnover process in response to DNA damage, as SDE2 prevented DNA damage arising from replication stress, and timely degradation of SDE2 allowed cell cycle progression and recovery from DNA damage to ensure cell survival. SDE2 was involved in regulating the DNA damage tolerance pathway by negatively regulating PCNA monoubiquitination, which was required for translesion DNA synthesis.
Using deletion screen in yeast with an Hub1 (UBL5; 606849) mutation, Thakran et al. (2018) identified Sde2 as a splicing factor that genetically interacted with Hub1. Yeast Sde2 is a conserved protein with a ubiquitin-fold and contains a GGKGG motif resembling the diglycine (GG) motif typical of the human UBL precursor. Sde2 was synthesized as a precursor in yeast, and the precursor was cleaved at the GGKGG motif to generate an N-terminal UBL fragment that played a regulatory role and a C-terminal fragment that was functional. Cleavage of Sde2 exposed the lysine residue at the N terminus of the Sde2 C-terminal fragment, allowing the fragment to be degraded via the N-end rule pathway. Sde2 UBL inhibited incorporation of the C-terminal fragment into the spliceosome, but processing of the UBL allowed association with the spliceosome. Functionally, the Sde2 C-terminal fragment was an intron-specific pre-mRNA splicing factor and was required for telomeric silencing and genomic stability. Further analysis indicated that the Sde2 C-terminal fragment facilitated association of Cactin (618536) with spliceosomes.
Rageul et al. (2019) demonstrated that the SDE2 C-terminal fragment generated from cleavage of the N-terminal UBL exposed the destabilizing residue lys at the N terminus of the C-terminal fragment. The lys was recognized by ubiquitin E3 ligases UBR1 (605981) and UBR2 (609134), leading to degradation of the C-terminal fragment in the arg/N-end rule pathway. Analysis of U2OS cells in response to UVC irradiation linked arg/N-end rule-regulated degradation of SDE2 C-terminal fragment to replication stress-induced ATR (601215) signaling. The SDE2 C-terminal fragment was phosphorylated in an ATR-dependent manner in response to UVC-induced replication stress, and phosphorylation promoted its association with the p97UFD1 (UFD1L; 601754)-NPL4 (NPLOC4; 606590) complex, leading to its chromatin-associated degradation. The N-end rule-dependent degradation of the SDE2 C-terminal fragment under replication stress promoted RPA (see 179835) phosphorylation and recovery from stalled forks for counteracting the replication stress, as timely degradation of the SDE2 fragment facilitated formation of single-stranded DNA (ssDNA) and signaling for DNA-damage bypass at stalled replication forks.
Rageul et al. (2020) demonstrated that SDE2 localized at active DNA replication forks in the nuclei of U2OS cells. SDE2 directly interacted with the C terminus of TIM (TIMELESS; 603887), a core component of the fork protection complex (FPC), via its SDE2 domain, forming an SDE2-TIM-TIPIN (610716) complex within the FPC. Through its interaction with TIM, SDE2 promoted stability of TIM to ensure integrity of the FPC at replication forks and replisome progression. SDE2 and TIM were also required for efficient fork progression and stalled fork recovery, efficient checkpoint activation, and protecting reversed forks from nucleolytic degradation. Further analysis demonstrated that SDE2-TIM interaction was essential for the FPC to carry out its roles in both DNA replication and protection of stalled forks from overresection.
By crosslinking and immunoprecipitation (CLIP) analyses, Floro et al. (2021) showed that SDE2 directly interacted with RNA, and that the interaction was almost entirely restricted to C/D box snoRNAs. By binding to snoRNAs, SDE2 regulated snoRNA-dependent rRNA cleavage and maturation of functional ribosomes, thereby playing a critical role in maintaining ribosome biogenesis and global protein synthesis in mammalian cells. In addition to rRNA processing, SDE2 functioned in pre-mRNA splicing, as it was present in a postcatalytic spliceosome complex, and depletion of SDE2 changed the patterns of pre-mRNA splicing and led to impairment of the cell cycle and cell death.
By mutation analysis, Weinheimer et al. (2022) showed that the SAP domain of SDE2 was a bona fide DNA-binding motif and was required for SDE2 localization at replication forks. SDE2 bound to both ssDNA and double-stranded DNA, but preferentially to ssDNA, and residues in the loop region of the SAP domain were important for DNA binding. However, the C-terminal tail (CTT) of SDE2 also contributed to SAP-dependent DNA binding. In corroboration, solution NMR structure revealed that the extended SDE2 SAP domain formed a helix-extended loop-helix motif connected to a unique CTT, and mutation analysis suggested that SAP and CTT together were responsible for DNA interactions by functioning as independent yet compulsory elements. This unique mode of DNA binding by SAT and CTT appeared to be generally applicable to other SAP-containing proteins, as SF3A3 (605596) also contained the unique extended SAP and CTT motif. Functional analysis demonstrated that the DNA-binding property of SDE2 mediated by the SAP domain was essential for its function at DNA replication forks, ensuring the integrity of the fork protection complex and fork stability via TIM regulation.
Floro, J., Dai, A., Metzger, A., Mora-Martin, A., Ganem, N. J., Cifuentes, D., Wu, C. S., Dalal, J., Lyons, S. M., Labadorf, A., Flynn, R. L. SDE2 is an essential gene required for ribosome biogenesis and the regulation of alternative splicing. Nucleic Acids Res. 49: 9424-9443, 2021. [PubMed: 34365507] [Full Text: https://doi.org/10.1093/nar/gkab647]
Gross, M. B. Personal Communication. Baltimore, Md. 3/1/2024.
Jo, U., Cai, W., Wang, J., Kwon, Y., D'Andrea, A. D., Kim, H. PCNA-dependent cleavage and degradation of SDE2 regulates response to replication stress. PLoS Genet. 12: e1006465, 2016. [PubMed: 27906959] [Full Text: https://doi.org/10.1371/journal.pgen.1006465]
Rageul, J., Park, J. J., Jo, U., Weinheimer, A. S., Vu, T. T. M., Kim, H. Conditional degradation of SDE2 by the arg/N-end rule pathway regulates stress response at replication forks. Nucleic Acids Res. 47: 3996-4010, 2019. [PubMed: 30698750] [Full Text: https://doi.org/10.1093/nar/gkz054]
Rageul, J., Park, J. J., Zeng, P. P., Lee, E. A., Yang, J., Hwang, S., Lo, N., Weinheimer, A. S., Scharer, O. D., Yeo, J. E., Kim, H. SDE2 integrates into the TIMELESS-TIPIN complex to protect stalled replication forks. Nature Commun. 11: 5495, 2020. [PubMed: 33127907] [Full Text: https://doi.org/10.1038/s41467-020-19162-5]
Sugioka-Sugiyama, R., Sugiyama, T. Sde2: a novel nuclear protein essential for telomeric silencing and genomic stability in Schizosaccharomyces pombe. Biochem. Biophys. Res. Commun. 406: 444-448, 2011. [PubMed: 21333630] [Full Text: https://doi.org/10.1016/j.bbrc.2011.02.068]
Thakran, P., Pandit, P. A., Datta, S., Kolathur, K. K., Pleiss, J. A., Mishra, S. K. Sde2 is an intron-specific pre-mRNA splicing regulator activated by ubiquitin-like processing. EMBO J. 37: 89-101, 2018. [PubMed: 28947618] [Full Text: https://doi.org/10.15252/embj.201796751]
Weinheimer, A. S., Paung, Y., Rageul, J., Khan, A., Lo, N., Ho, B., Tong, M., Alphonse, S., Seeliger, M. A., Kim, H. Extended DNA-binding interfaces beyond the canonical SAP domain contribute to the function of replication stress regulator SDE2 at DNA replication forks. J. Biol. Chem. 298: 102268, 2022. [PubMed: 35850305] [Full Text: https://doi.org/10.1016/j.jbc.2022.102268]