Alternative titles; symbols
HGNC Approved Gene Symbol: UBE2I
Cytogenetic location: 16p13.3 Genomic coordinates (GRCh38): 16:1,309,152-1,327,017 (from NCBI)
The ubiquitin-conjugating enzymes (E2s) are a family of proteins involved in the ubiquitin-dependent protein degradation system. In yeast, at least 10 different E2s have been identified; they are involved in essential cellular processes such as DNA repair, cell cycle control, and stress responses. Using the yeast 2-hybrid system with the repressor domain of the Wilms tumor gene product (WT1; 607102) as bait, Wang et al. (1996) isolated a cDNA encoding a human homolog of the yeast ubiquitin-conjugating enzyme-9 (UBC9). Human UBC9 has 56% identity with yeast ubc9 and contains the active site cysteine necessary for the ubiquitin-conjugating activity of all E2 enzymes. Northern blot analysis revealed human UBC9 transcripts of 4.4, 2.4, and 1.3 kb in all of the tissues examined.
Watanabe et al. (1996) likewise cloned UBE2I, a human homolog of yeast ubc9. The deduced protein contains 158 amino acids.
Yasugi and Howley (1996) independently isolated the human UBC9 gene.
Nacerddine et al. (2005) stated that the human and mouse UBC9 proteins are 100% identical. Rajan et al. (2005) stated that the human and Xenopus UBC9 proteins are identical.
Wang et al. (1996) found that human UBC9 could fully complement the mutant phenotype of a yeast ubc9 mutant strain. In yeast, ubc9 is involved in cell cycle progression via degradation of cyclins (see 123835). Wang et al. (1996) suggested that human UBC9 may play a similar role via interaction with WT1, which is able to impose a block to cell cycle progression in eukaryotic cells.
Yasugi and Howley (1996) found that human UBC9 could support the growth of yeast ubc9 temperature-sensitive mutants at nonpermissive temperatures, indicating that the gene is a functional homolog of yeast ubc9.
A sumoylated form of RANGAP1 (602362) associates with the nuclear pore complex and is required for import of proteins into the nucleus. Okuma et al. (1999) showed that SUA1 (SAE1; 613294), UBA2 (613295), and UBC9 catalyzed in vitro sumoylation of RANGAP1. Faint RANGAP1 modification was observed in the absence of UBC9. Okuma et al. (1999) concluded that, in contrast to the 3-step ubiquitination reaction, which requires an E1 ubiquitin-activating enzyme, an E2 ubiquitin-conjugating enzyme, and an E3 ubiquitin ligase, sumoylation is a 2-step reaction in which the SUA1/UBA2 dimer functions as an E1 enzyme and UBC9 functions as an E2 enzyme.
Fragile histidine triad (FHIT; 601153), a candidate tumor suppressor gene located on 3p14.2, is deleted in many types of human cancer. Using a yeast 2-hybrid screen to search for proteins that interact with the FHIT protein in vivo, Shi et al. (2000) found that UBC9 is specifically associated with FHIT. The last 21 amino acids at the C terminus of UBC9 appear to be unimportant for its biologic activity, since a UBC9 mutant harboring a deletion of these amino acids could still restore normal growth of yeast containing a temperature-sensitive mutation in the homolog UBC9 gene. Mutational analysis indicated that UBC9 was associated with the C-terminal portion of FHIT. The interaction between FHIT and UBC9 appeared to be independent of the enzymatic activity of FHIT. Given that yeast UBC9 is involved in the degradation of S- and M-phase cyclins, Shi et al. (2000) concluded that FHIT may be involved in cell cycle control through its interaction with UBC9.
The RAD6 (179095) pathway is central to postreplicative DNA repair in eukaryotic cells. Two principal elements of this pathway are the ubiquitin-conjugating enzymes RAD6 and the MMS2 (603001)-UBC13 (603679) heterodimer, which are recruited to chromatin by the RING finger proteins RAD18 (605256) and RAD5 (608048), respectively. Hoege et al. (2002) showed that UBC9, a small ubiquitin-related modifier (SUMO)-conjugating enzyme, is also affiliated with this pathway and that proliferating cell nuclear antigen (PCNA; 176740), a DNA polymerase sliding clamp involved in DNA synthesis and repair, is a substrate. PCNA is monoubiquitinated through RAD6 and RAD18, modified by lys63-linked multiubiquitination, which additionally requires MMS2, UBC13, and RAD5, and is conjugated to SUMO by UBC9. All 3 modifications affect the same lysine residue of PCNA, K164, suggesting that they label PCNA for alternative functions. Hoege et al. (2002) demonstrated that these modifications differentially affect resistance to DNA damage, and that damage-induced PCNA ubiquitination is elementary for DNA repair and occurs at the same conserved residue in yeast and humans.
Rajan et al. (2005) found that the potassium channel K2P1 (KCNK1; 601745) was sumoylated on intracellular lys274 by Xenopus or human UBC9 at the cell surface, and that sumoylation rendered the channel inactive. Mutation of lys274 or desumoylation of K2P1 by SENP1 (612157) activated the pore, which functioned as a potassium leak channel.
Carbia-Nagashima et al. (2007) found that overexpression of human RSUME (RWDD3; 615875) in COS-7 cells increased overall protein sumoylation. In vitro, RSUME increased UBC9-dependent SUMO1 conjugation to target proteins both by enhancing the formation of the UBC9-SUMO1 thioester and by enhancing the transfer of SUMO1 from the thioester to the substrate protein. RSUME enhanced sumoylation of I-kappa-B (see 164008), leading to inhibition of NF-kappa-B (see 164011) transcriptional activity, and of HIF1A (603348), leading to HIF1A stabilization during hypoxia. Carbia-Nagashima et al. (2007) concluded that RSUME enhances sumoylation of proteins by UBC9.
Using immunoblot and proteomic analyses, Ribet et al. (2010) observed a decrease in both SUMO1 (601912)- and SUMO2 (603042)/SUMO3 (602231)-conjugated proteins of high molecular mass in HeLa cells infected with Listeria monocytogenes (Lm). The decrease was not observed in cells infected with nonpathogenic L. inocula or with Lm defective for listeriolysin (LLO) toxin, and LLO alone triggered a massive decrease in sumoylated proteins in HeLa and Jeg3 cells. Treatment with LLO alone or infection with wildtype Lm led to a dramatic decrease in the level of UBC9, but not of SAE1 or SAE2 (UBA2). The decrease in UBC9 resulted from degradation of the enzyme rather than altered translation and required LLO binding to cellular membranes and pore formation. Perfringolysin O and pneumolysin, LLO-like pore-forming toxins encoded by other bacterial pathogens, also triggered degradation of UBC9. Overexpression of SUMO1 or SUMO2 in HeLa cells impaired Lm infection. Ribet et al. (2010) concluded that Listeria, and probably other pathogens, dampen the host response by decreasing the sumoylation level of proteins critical for infection by targeting UBC9, an essential enzyme of the SUMO pathway.
Crystal Structure
Bernier-Villamor et al. (2002) performed crystallographic analysis of a complex between mammalian UBC9 and a C-terminal domain of RANGAP1 (602362) at 2.5 angstroms. These experiments revealed structural determinants for recognition of consensus SUMO (SUMO1; 601912) modification sequences found within SUMO-conjugated proteins. Structure-based mutagenesis and biochemical analysis of UBC9 and RANGAP1 revealed distinct motifs required for substrate binding and SUMO modification of p53 (191170), NFKBIA (164008), and RANGAP1.
Reverter and Lima (2005) described the 3.0-angstrom crystal structure of a 4-protein complex of UBC9, a NUP358/RANBP2 (601181) E3 ligase domain (IR1-M), and SUMO1 conjugated to the carboxy-terminal domain of RANGAP1. Structural insights, combined with biochemical and kinetic data obtained with additional substrates, supported a model in which NUP358/RANBP2 acts as an E3 by binding both SUMO and UBC9 to position the SUMO-E2-thioester in an optimal orientation to enhance conjugation.
Nacerddine et al. (2005) determined that the mouse Ubc9 gene contains 7 exons.
By fluorescence in situ hybridization (FISH), Wang et al. (1996) mapped the human UBC9 gene to chromosome 16p13.3. Watanabe et al. (1996) mapped UBE2I to 16p13.3 by FISH. Tachibana et al. (1996) also mapped UBE2I to 16p13.3 by FISH.
To investigate the significance of the SUMO system in mammals, Nacerddine et al. (2005) generated mice deficient for the Ubc9 protein. They found that expression of a single Ubc9 allele was sufficient to generate a normal pattern of Sumo1-conjugated proteins; however, homozygous Ubc9 deficiency resulted in embryonic lethality. Ubc9-null embryos died early in development, subsequent to the blastocyst stage and prior to embryonic day 7.5. In culture, mutant blastocysts were viable for up to 2 days, but thereafter showed apoptosis of the inner cell mass. Mutant cells developed chromosome defects and gross alterations in nuclear organization such as disassembled nucleoli, PML (102578)-positive nuclear bodies, and misshapen nuclei, as well as mislocalized Ran (601179) and RanGAP1 (602362). Nacerddine et al. (2005) concluded that UBC9, and by implication, the SUMO pathway, are crucial for proper nuclear architecture, accurate chromosome segregation, and embryonic viability.
Bernier-Villamor, V., Sampson, D. A., Matunis, M. J., Lima, C. D. Structural basis for E2-mediated SUMO conjugation revealed by a complex between ubiquitin-conjugating enzyme Ubc9 and RanGAP1. Cell 108: 345-356, 2002. [PubMed: 11853669] [Full Text: https://doi.org/10.1016/s0092-8674(02)00630-x]
Carbia-Nagashima, A., Gerez, J., Perez-Castro, C., Paez-Pereda, M., Silberstein, S., Stalla, G. K., Holsboer, F., Arzt, E. RSUME, a small RWD-containing protein, enhances SUMO conjugation and stabilizes HIF-1-alpha during hypoxia. Cell 131: 309-323, 2007. [PubMed: 17956732] [Full Text: https://doi.org/10.1016/j.cell.2007.07.044]
Hoege, C., Pfander, B., Moldovan, G.-L., Pyrowolakis, G., Jentsch, S. RAD6-dependent DNA repair is linked to modification of PCNA by ubiquitin and SUMO. Nature 419: 135-141, 2002. [PubMed: 12226657] [Full Text: https://doi.org/10.1038/nature00991]
Nacerddine, K., Lehembre, F., Bhaumik, M., Artus, J., Cohen-Tannoudji, M., Babinet, C., Pandolfi, P. P., Dejean, A. The SUMO pathway is essential for nuclear integrity and chromosome segregation in mice. Dev. Cell 9: 769-779, 2005. [PubMed: 16326389] [Full Text: https://doi.org/10.1016/j.devcel.2005.10.007]
Okuma, T., Honda, R., Ichikawa, G., Tsumagari, N., Yasuda, H. In vitro SUMO-1 modification requires two enzymatic steps, E1 and E2. Biochem. Biophys. Res. Commun. 254: 693-698, 1999. [PubMed: 9920803] [Full Text: https://doi.org/10.1006/bbrc.1998.9995]
Rajan, S., Plant, L. D., Rabin, M. L., Butler, M. H., Goldstein, S. A. N. Sumoylation silences the plasma membrane leak K(+) channel K2P1. Cell 121: 37-47, 2005. Note: Erratum: Cell 141: 368 only, 2010. [PubMed: 15820677] [Full Text: https://doi.org/10.1016/j.cell.2005.01.019]
Reverter, D., Lima, C. D. Insights into E3 ligase activity revealed by a SUMO-RanGAP1-Ubc9-Nup358 complex. (Letter) Nature 435: 687-692, 2005. [PubMed: 15931224] [Full Text: https://doi.org/10.1038/nature03588]
Ribet, D., Hamon, M., Gouin, E., Nahori, M.-A., Impens, F., Neyret-Kahn, H., Gevaert, K., Vandekerckhove, J., Dejean, A., Cossart, P. Listeria monocytogenes impairs SUMOylation for efficient infection. Nature 464: 1192-1195, 2010. Note: Erratum: Nature 580: E20, 2020. [PubMed: 20414307] [Full Text: https://doi.org/10.1038/nature08963]
Shi, Y., Zou, M., Farid, N. R., Paterson, M. C. Association of FHIT (fragile histidine triad), a candidate tumour suppressor gene, with the ubiquitin-conjugating enzyme hUBC9. Biochem. J. 352: 443-448, 2000. [PubMed: 11085938]
Tachibana, M., Iwata, N., Watanabe, A., Nobukuni, Y., Ploplis, B., Kajigaya, S. Assignment of the gene for a ubiquitin-conjugating enzyme (UBE2I) to human chromosome band 16p13.3 by in situ hybridization. Cytogenet. Cell Genet. 75: 222-223, 1996. [PubMed: 9067428] [Full Text: https://doi.org/10.1159/000134487]
Wang, Z.-Y., Qiu, Q.-Q., Seufert, W., Taguchi, T., Testa, J. R., Whitmore, S. A., Callen, D. F., Welsh, D., Shenk, T., Deuel, T. F. Molecular cloning of the cDNA and chromosome localization of the gene for human ubiquitin-conjugating enzyme 9. J. Biol. Chem. 271: 24811-24816, 1996. [PubMed: 8798754] [Full Text: https://doi.org/10.1074/jbc.271.40.24811]
Watanabe, T. K., Fujiwara, T., Kawai, A., Shimizu, F., Takami, S., Hirano, H., Okuno, S., Ozaki, K., Takeda, S., Shimada, Y., Nagata, M., Takaichi, A., Takahashi, E., Nakamura, Y., Shin, S. Cloning, expression, and mapping of UBE2I, a novel gene encoding a human homologue of yeast ubiquitin-conjugating enzymes which are critical for regulating the cell cycle. Cytogenet. Cell Genet. 72: 86-89, 1996. [PubMed: 8565643] [Full Text: https://doi.org/10.1159/000134169]
Yasugi, T., Howley, P. M. Identification of the structural and functional human homolog of the yeast ubiquitin conjugating enzyme UBC9. Nucleic Acids Res. 24: 2005-2010, 1996. [PubMed: 8668529] [Full Text: https://doi.org/10.1093/nar/24.11.2005]