Small Ubiquitin-like Modifier (or SUMO) proteins are a family of small proteins that are covalently attached to and detached from other proteins in cells to modify their function. SUMOylation is a post-translational modification involved in various cellular processes, such as nuclear-cytosolic transport, transcriptional regulation, apoptosis, protein stability, response to stress, and progression through the cell cycle.
SUMO proteins are similar to ubiquitin, and SUMOylation is directed by an enzymatic cascade analogous to that involved in ubiquitination. In contrast to ubiquitin, SUMO is not used to tag proteins for degradation. Mature SUMO is produced when the last four amino acids of the C-terminus have been cleaved off to allow formation of an isopeptide bond between the C-terminal glycine residue of SUMO and an acceptor lysine on the target protein.
SUMO modification of proteins has many functions. Among the most frequent and best studied are protein stability, nuclear-cytosolic transport, and transcriptional regulation. Typically, only a small fraction of a given protein is SUMOylated and this modification is rapidly reversed by the action of deSUMOylating enzymes. SUMOylation of target proteins has been shown to cause a number of different outcomes including altered localization and binding partners. The SUMO-1 modification of RanGAP1 (the first identified SUMO substrate) leads to its trafficking from cytosol to nuclear pore complex. The SUMO modification of hNinein leads to its movement from the centrosome to the nucleus. In many cases, SUMO modification of transcriptional regulators correlates with inhibition of transcription. One can refer to the GeneRIFs of the SUMO proteins, e.g. human SUMO-1, to find out more.
There are 4 confirmed SUMO isoforms in humans; SUMO-1, SUMO-2, SUMO-3 and SUMO-4. SUMO-2/3 show a high degree of similarity to each other and are distinct from SUMO-1. SUMO-4 shows similarity to SUMO-2/3 but differs in having a Proline instead of Glutamine at position 90. As a result, SUMO-4 isn't processed and conjugated under normal conditions, but is used for modification of proteins under stress-conditions like starvation. During mitosis, SUMO-2/3 localize to centromeres and condensed chromosomes, whereas SUMO-1 localizes to the mitotic spindle and spindle midzone, indicating that SUMO paralogs regulate distinct mitotic processes in mammalian cells. One of the major SUMO conjugation products associated with mitotic chromosomes arose from SUMO-2/3 conjugation of topoisomerase II, which is modified exclusively by SUMO-2/3 during mitosis. SUMO-2/3 modifications seem to be involved specifically in the stress response. SUMO-1 and SUMO-2/3 can form mixed chains, however, because SUMO-1 does not contain the internal SUMO consensus sites found in SUMO-2/3, it is thought to terminate these poly-SUMO chains. Serine 2 of SUMO-1 is phosphorylated, raising the concept of a 'modified modifier'.
SUMO proteins are small; most are around 100 amino acids in length and 12 kDa in mass. The exact length and mass varies between SUMO family members and depends on which organism the protein comes from. Although SUMO has very little sequence identity with ubiquitin at the amino acid level, it has a nearly identical structural fold.
The structure of human SUMO1 is depicted on the right. It shows SUMO1 as a globular protein with both ends of the amino acid chain (shown in red and blue) sticking out of the protein's centre. The spherical core consists of an alpha helix and a beta sheet. The diagrams shown are based on an NMR analysis of the protein in solution.
Prediction of SUMO attachment
Most SUMO-modified proteins contain the tetrapeptide consensus motif Ψ-K-x-D/E where Ψ is a hydrophobic residue, K is the lysine conjugated to SUMO, x is any amino acid (aa), D or E is an acidic residue. Substrate specificity appears to be derived directly from Ubc9 and the respective substrate motif. Currently available prediction programs are:
- SUMOplot - online free access software developed to predict the probability for the SUMO consensus sequence (SUMO-CS) to be engaged in SUMO attachment. The SUMOplot score system is based on two criteria: 1) direct amino acid match to the SUMO-CS observed and shown to bind Ubc9, and 2) substitution of the consensus amino acid residues with amino acid residues exhibiting similar hydrophobicity. SUMOplot has been used in the past to predict Ubc9 dependent sites.
- seeSUMO - uses random forests and support vector machines trained on the data collected from the literature
- SUMOsp - uses PSSM to score potential sumoylation peptide stites. It can predict sites followed the ψKXE motif and unusual sumoylation sites contained other non-canonical motifs.
- JASSA - online free access predictor of SUMOylation sites (classical and inverted consensus) and SIMs (SUMO interacting motif). JASSA uses a scoring system based on a Position Frequency Matrix derived from the alignment of experimental SUMOylation sites or SIMs. Novel features were implemented towards a better evaluation of the prediction, including identification of database hits matching the query sequence and representation of candidate sites within the secondary structural elements and/or the 3D fold of the protein of interest, retrievable from deposited PDB files.
SUMO attachment to its target is similar to that of ubiquitin (as it is for the other ubiquitin-like proteins such as NEDD 8). A C-terminal peptide is cleaved from SUMO by a protease (in human these are the SENP proteases or Ulp1 in yeast) to reveal a di-glycine motif. SUMO then becomes bound to an E1 enzyme (SUMO Activating Enzyme (SAE)) which is a heterodimer. It is then passed to an E2 which is a conjugating enzyme (Ubc9). Finally, one of a small number of E3 ligating proteins attaches it to the protein. In yeast, there are four SUMO E3 proteins, Cst9, Mms21, Siz1 and Siz2. While in ubiquitination an E3 is essential to add ubiquitin to its target, evidence suggests that the E2 is sufficient in Sumoylation as long as the consensus sequence is present. It is thought that the E3 ligase promotes the efficiency of sumoylation and in some cases has been shown to direct SUMO conjugation onto non-consensus motifs. E3 enzymes can be largely classed into PIAS proteins, such as Mms21 (a member of the Smc5/6 complex) and Pias-gamma and HECT proteins. Some E3's such as RanBP2 however are neither. Recent evidence has shown that PIAS-gamma is required for the sumoylation of the transcription factor yy1 but it is independent of the zinc-RING finger (identified as the functional domain of the E3 ligases). SUMOylation is reversible and is removed from targets by specific SUMO proteases. In budding yeast, the Ulp1 SUMO protease is found bound at the nuclear pore, whereas Ulp2 is nucleoplasmic. The distinct subnuclear localisation of deSUMOylating enzymes is conserved in higher eukaryotes.
- Hay RT (Apr 2005). "SUMO: a history of modification". Mol. Cell 18 (1): 1–12. doi:10.1016/j.molcel.2005.03.012. PMID 15808504.
- Matunis MJ, Coutavas E, Blobel G (Dec 1996). "A novel ubiquitin-like modification modulates the partitioning of the Ran-GTPase-activating protein RanGAP1 between the cytosol and the nuclear pore complex". J Cell Biol. 135 (6 Pt 1): 1457–70. doi:10.1083/jcb.135.6.1457. PMC 2133973. PMID 8978815.
- Mahajan R, Delphin C, Guan T, Gerace L, Melchior F (Jan 1997). "A small ubiquitin-related polypeptide involved in targeting RanGAP1 to nuclear pore complex protein RanBP2". Cell 88 (1): 97–107. doi:10.1016/S0092-8674(00)81862-0. PMID 9019411.
- Cheng TS, Chang LK, Howng SL, Lu PJ, Lee CI, Hong YR (Feb 2006). "SUMO-1 modification of centrosomal protein hNinein promotes hNinein nuclear localization". Life Sci. 78 (10): 1114–20. doi:10.1016/j.lfs.2005.06.021. PMID 16154161.
- Gill G (Oct 2005). "Something about SUMO inhibits transcription". Current Opinion in Genetics & Development 15 (5): 536–41. doi:10.1016/j.gde.2005.07.004. PMID 16095902.
- SUMO1 SMT3 suppressor of mif two 3 homolog 1 (S. cerevisiae)
- Wei W, Yang P, Pang J, Zhang S, Wang Y, Wang M, Dong Z She J, Wang C (Oct 2008). "A stress-dependent SUMO4 sumoylation of its substrate proteins". Biochem Biophys Res Commun 375 (3): 454–459. doi:10.1016/j.bbrc.2008.08.028. PMID 18708028.
- Zhang XD, Goeres J, Zhang H, Yen TJ, Porter AC, Matunis MJ (Mar 2008). "SUMO-2/3 Modification and Binding Regulate the Association of CENP-E with Kinetochores and Progression through Mitosis". Mol Cell 29 (6): 729–41. doi:10.1016/j.molcel.2008.01.013. PMC 2366111. PMID 18374647.
- Azuma Y, Arnaoutov A, Dasso M (Nov 2003). "SUMO-2/3 regulates topoisomerase II in mitosis". J Cell Biol. 163 (3): 477–87. doi:10.1083/jcb.200304088. PMC 2173648. PMID 14597774.
- Saitoh H, Hinchey J (Mar 2000). "Functional heterogeneity of small ubiquitin-related protein modifiers SUMO-1 versus SUMO-2/3". J Biol Chem. 275 (9): 6252–8. doi:10.1074/jbc.275.9.6252. PMID 10692421.
- Matic I, van Hagen M, Schimmel J, et al. (Jan 2008). "In vivo identification of human small ubiquitin-like modifier polymerization sites by high accuracy mass spectrometry and an in vitro to in vivo strategy". Mol Cell Proteomics. 7 (1): 132–44. doi:10.1074/mcp.M700173-MCP200. PMC 3840926. PMID 17938407.
- Matic I, Macek B, Hilger M, Walther TC, Mann M (Sep 2008). "Phosphorylation of SUMO-1 occurs in vivo and is conserved through evolution". J Proteome Res. 7 (9): 4050–7. doi:10.1021/pr800368m. PMID 18707152.
- Gramatikoff K. et al. In Frontiers of Biotechnology and Pharmaceuticals, Science Press (2004) 4: pp.181-210.
- Teng, S.; Luo, H.; Wang, L. (2011). "Predicting protein sumoylation sites from sequence features". Amino Acids 43 (1): 447–455. doi:10.1007/s00726-011-1100-2. PMID 21986959.
- Ren, J.; Gao, X.; Jin, C.; Zhu, M.; Wang, X.; Shaw, A.; Wen, L.; Yao, X.; Xue, Y. (2009). "Systematic study of protein sumoylation: Development of a site-specific predictor of SUMOsp 2.0". Proteomics 9 (12): 3409–3412. doi:10.1002/pmic.200800646. PMID 19504496.
- Beauclair, G; Bridier-Nahmias, A; Zagury, J. F.; Saïb, A; Zamborlini, A (2015). "JASSA: A comprehensive tool for prediction of SUMOylation sites and SIMs". Bioinformatics 31 (21): 3483–91. doi:10.1093/bioinformatics/btv403. PMID 26142185.
- Cheng CH, Lo YH, Liang SS, et al. (Aug 2006). "SUMO modifications control assembly of synaptonemal complex and polycomplex in meiosis of Saccharomyces cerevisiae". Genes Dev. 20 (15): 2067–81. doi:10.1101/gad.1430406. PMC 1536058. PMID 16847351.
- Pichler A, Knipscheer P, Saitoh H, Sixma TK, Melchior F (Oct 2004). "The RanBP2 SUMO E3 ligase is neither HECT- nor RING-type". Nature Structural & Molecular Biology 11 (10): 984–91. doi:10.1038/nsmb834. PMID 15378033.
- Mukhopadhyay D, Dasso M (Jun 2007). "Modification in reverse: the SUMO proteases". Trends Biochem. Sci. 32 (6): 286–95. doi:10.1016/j.tibs.2007.05.002. PMID 17499995.
- Ulrich HD (Oct 2005). "Mutual interactions between the SUMO and ubiquitin systems: a plea of no contest". Trends Cell Biol. 15 (10): 525–532. doi:10.1016/j.tcb.2005.08.002. PMID 16125934.
- Gill G (Oct 2005). "Something about SUMO inhibits transcription". Current Opinion in Genetics & Development 15 (5): 536–541. doi:10.1016/j.gde.2005.07.004. PMID 16095902.
- Li M, Guo D, Isales CM, et al. (Jul 2005). "SUMO wrestling with type 1 diabetes". J. Mol. Med. 83 (7): 504–513. doi:10.1007/s00109-005-0645-5. PMID 15806321.
- Verger A, Perdomo J, Crossley M (Feb 2003). "Modification with SUMO: A role in transcriptional regulation". EMBO Rep. 4 (2): 137–142. doi:10.1038/sj.embor.embor738. PMC 1315836. PMID 12612601.
- Peroutka III RJ, Orcutt SJ, Strickler JE, Butt TR (2011). "SUMO fusion technology for enhanced protein expression and purification in prokaryotes and eukaryotes". Methods Mol. Biol: Heterologous gene expression in E. Coli. Methods in Molecular Biology 705: 15–30. doi:10.1007/978-1-61737-967-3_2. ISBN 978-1-61737-966-6. PMID 21125378.
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- LifeSensors' SUMO-based Protein and Peptide Expression Systems
- Proteins Expressed With SUMO
- Boston Biochem overview of SUMO reagents and the SUMOylation Cycle
- SUMO1 homology group from HomoloGene
- human SUMO proteins on ExPASy: SUMO1 SUMO2 SUMO3 SUMO4
- UniProt entry for rat Sumo1
Programs for prediction sumoylation:
- SUMOplot Analysis Program — predicts and scores sumoylation sites in your protein (by Abgent)
- seeSUMO - prediction of sumoulation sites
- SUMOsp - prediction of sumoulation sites
- JASSA - Predicts and scores SUMOylation sites and SIM (SUMO interacting motif)