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Antila CJM, Rraklli V, Blomster HA, Dahlström KM, Salminen TA, Holmberg J, Sistonen L, Sahlgren C. Sumoylation of Notch1 represses its target gene expression during cell stress. Cell Death Differ 2018; 25:600-615. [PMID: 29305585 PMCID: PMC5864205 DOI: 10.1038/s41418-017-0002-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 09/08/2017] [Accepted: 09/11/2017] [Indexed: 02/06/2023] Open
Abstract
The Notch signaling pathway is a key regulator of stem cells during development, and its deregulated activity is linked to developmental defects and cancer. Transcriptional activation of Notch target genes requires cleavage of the Notch receptor in response to ligand binding, production of the Notch intracellular domain (NICD1), NICD1 migration into the nucleus, and assembly of a transcriptional complex. Post-translational modifications of Notch regulate its trafficking, turnover, and transcriptional activity. Here, we show that NICD1 is modified by small ubiquitin-like modifier (SUMO) in a stress-inducible manner. Sumoylation occurs in the nucleus where NICD1 is sumoylated in the RBPJ-associated molecule (RAM) domain. Although stress and sumoylation enhance nuclear localization of NICD1, its transcriptional activity is attenuated. Molecular modeling indicates that sumoylation can occur within the DNA-bound ternary transcriptional complex, consisting of NICD1, the transcription factor Suppressor of Hairless (CSL), and the co-activator Mastermind-like (MAML) without its disruption. Mechanistically, sumoylation of NICD1 facilitates the recruitment of histone deacetylase 4 (HDAC4) to the Notch transcriptional complex to suppress Notch target gene expression. Stress-induced sumoylation decreases the NICD1-mediated induction of Notch target genes, which was abrogated by expressing a sumoylation-defected mutant in cells and in the developing central nervous system of the chick in vivo. Our findings of the stress-inducible sumoylation of NICD1 reveal a novel context-dependent regulatory mechanism of Notch target gene expression.
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Affiliation(s)
- Christian J M Antila
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, FI-20520, Turku, Finland.,Faculty of Science and Engineering, Åbo Akademi University, FI-20520, Turku, Finland
| | - Vilma Rraklli
- Department of Cell and Molecular Biology, Karolinska Institutet, 285 SE-171 77, Stockholm, Sweden
| | - Henri A Blomster
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, FI-20520, Turku, Finland.,Faculty of Science and Engineering, Åbo Akademi University, FI-20520, Turku, Finland
| | - Käthe M Dahlström
- Faculty of Science and Engineering, Åbo Akademi University, FI-20520, Turku, Finland
| | - Tiina A Salminen
- Faculty of Science and Engineering, Åbo Akademi University, FI-20520, Turku, Finland
| | - Johan Holmberg
- Department of Cell and Molecular Biology, Karolinska Institutet, 285 SE-171 77, Stockholm, Sweden
| | - Lea Sistonen
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, FI-20520, Turku, Finland.,Faculty of Science and Engineering, Åbo Akademi University, FI-20520, Turku, Finland
| | - Cecilia Sahlgren
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, FI-20520, Turku, Finland. .,Faculty of Science and Engineering, Åbo Akademi University, FI-20520, Turku, Finland. .,Department of Biomedical Engineering, Technical University of Eindhoven, 5613 DR, Eindhoven, The Netherlands.
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Blomster HA, Imanishi SY, Siimes J, Kastu J, Morrice NA, Eriksson JE, Sistonen L. In vivo identification of sumoylation sites by a signature tag and cysteine-targeted affinity purification. J Biol Chem 2010; 285:19324-9. [PMID: 20388717 DOI: 10.1074/jbc.m110.106955] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Small ubiquitin-like modifier (SUMO) is conjugated to its substrates via an enzymatic cascade consisting of three enzymes, E1, E2, and E3. The active site of the E2 enzyme, Ubc9, recognizes the substrate through binding to a consensus tetrapeptide PsiKXE. However, recent proteomics studies suggested that a considerable part of sumoylation occurs on non-consensus sites. Current unbiased sumoylation site identification techniques typically require high stoichiometry in vitro sumoylation, mass spectrometry, and complex data analysis. To facilitate in vivo analysis, we have designed a mass spectrometric method based on an engineered human SUMO-1 construct that creates a signature tag on SUMO substrates. This construct enables affinity purification by covalent binding to cysteine residues in LysC/trypsin-cleaved peptides and site identification by diglycyl lysine tagging of sumoylation sites. As a proof of concept, site-specific and substrate-unbiased in vivo sumoylation analysis of HeLa cells was performed. We identified 14 sumoylation sites, including well known sites, such as Lys(524) of RanGAP1, and novel non-consensus sites. Only 3 of the 14 sites matched consensus sites, supporting the emerging view that non-consensus sumoylation is a common event in live cells. Six of the non-consensus sites had a nearby SUMO interaction motif (SIM), which emphasizes the role of SIM in non-consensus sumoylation. Nevertheless, the lack of nearby SIM residues among the remaining non-consensus sites indicates that there are also other specificity determinants of non-consensus sumoylation. The method we have developed proved to be a useful tool for sumoylation studies and will facilitate identification of novel SUMO substrates containing both consensus and non-consensus sites.
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Affiliation(s)
- Henri A Blomster
- From the Department of Biosciences, Abo Akademi University, FI-20520 Turku, Finland
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Blomster HA, Hietakangas V, Wu J, Kouvonen P, Hautaniemi S, Sistonen L. Novel proteomics strategy brings insight into the prevalence of SUMO-2 target sites. Mol Cell Proteomics 2009; 8:1382-90. [PMID: 19240082 DOI: 10.1074/mcp.m800551-mcp200] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Small ubiquitin-like modifier (SUMO) is covalently conjugated to its target proteins thereby altering their activity. The mammalian SUMO protein family includes four members (SUMO-1-4) of which SUMO-2 and SUMO-3 are conjugated in a stress-inducible manner. The vast majority of known SUMO substrates are recognized by the single SUMO E2-conjugating enzyme Ubc9 binding to a consensus tetrapeptide (PsiKXE where Psi stands for a large hydrophobic amino acid) or extended motifs that contain phosphorylated or negatively charged amino acids called PDSM (phosphorylation-dependent sumoylation motif) and NDSM (negatively charged amino acid-dependent sumoylation motif), respectively. We identified 382 SUMO-2 targets using a novel method based on SUMO protease treatment that improves separation of SUMO substrates on SDS-PAGE before LC-ESI-MS/MS. We also implemented a software SUMOFI (SUMO motif finder) to facilitate identification of motifs for SUMO substrates from a user-provided set of proteins and to classify the substrates according to the type of SUMO-targeting consensus site. Surprisingly more than half of the substrates lacked any known consensus site, suggesting that numerous SUMO substrates are recognized by a yet unknown consensus site-independent mechanism. Gene ontology analysis revealed that substrates in distinct functional categories display strikingly different prevalences of NDSM sites. Given that different types of motifs are bound by Ubc9 using alternative mechanisms, our data suggest that the preference of SUMO-2 targeting mechanism depends on the biological function of the substrate.
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Affiliation(s)
- Henri A Blomster
- Department of Biology, Abo Akademi University and University of Turku, FI-20521 Turku, Finland
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Hietakangas V, Anckar J, Blomster HA, Fujimoto M, Palvimo JJ, Nakai A, Sistonen L. PDSM, a motif for phosphorylation-dependent SUMO modification. Proc Natl Acad Sci U S A 2005; 103:45-50. [PMID: 16371476 PMCID: PMC1324973 DOI: 10.1073/pnas.0503698102] [Citation(s) in RCA: 381] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
SUMO (small ubiquitin-like modifier) modification regulates many cellular processes, including transcription. Although sumoylation often occurs on specific lysines within the consensus tetrapeptide PsiKxE, other modifications, such as phosphorylation, may regulate the sumoylation of a substrate. We have discovered PDSM (phosphorylation-dependent sumoylation motif), composed of a SUMO consensus site and an adjacent proline-directed phosphorylation site (PsiKxExxSP). The highly conserved motif regulates phosphorylation-dependent sumoylation of multiple substrates, such as heat-shock factors (HSFs), GATA-1, and myocyte enhancer factor 2. In fact, the majority of the PDSM-containing proteins are transcriptional regulators. Within the HSF family, PDSM is conserved between two functionally distinct members, HSF1 and HSF4b, whose transactivation capacities are repressed through the phosphorylation-dependent sumoylation. As the first recurrent sumoylation determinant beyond the consensus tetrapeptide, the PDSM provides a valuable tool in predicting new SUMO substrates.
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Affiliation(s)
- Ville Hietakangas
- Turku Centre for Biotechnology, University of Turku and Abo Akademi University, FI-20521, Turku, Finland
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