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Interferon-induced global cellular SUMOylation Changes

ABSTRACT: This proteomics dataset was generated to study the changes in SUMO site abundances between control cells and Interferon-alpha treated cells using SILAC. Cells were first fractionated into the cytoplasmic and nuclear fractions. SUMOylated proteins were then purified from these extracts by Ni-NTA via the 6xHIS tag on the SUMO3 construct. The proteins were then digested with trypsin and the peptides desalted on HLB cartridges. The SUMOylated peptides, which harbor an NQTGG remnant after tryptic digestion, were enriched with our anti-NQTGG antibody. The resulting peptides were injected on the orbitrap fusion instrument. The .raw files were analyzed with maxqunt.

INSTRUMENT(S): Orbitrap Fusion ETD

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Mounira K. Chelbi-Alix Pierre Thibault

PROVIDER: MSV000081525 | MassIVE |

SECONDARY ACCESSION(S): PXD007730

REPOSITORIES: MassIVE

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Promyelocytic Leukemia Protein (PML) Requirement for Interferon-induced Global Cellular SUMOylation.

Maroui Mohamed Ali MA Maarifi Ghizlane G McManus Francis P FP Lamoliatte Frédéric F Thibault Pierre P Chelbi-Alix Mounira K MK

Molecular & cellular proteomics : MCP 20180313 6

We report that interferon (IFN) α treatment at short and long periods increases the global cellular SUMOylation and requires the presence of the SUMO E3 ligase promyelocytic leukemia protein (PML), the organizer of PML nuclear bodies (NBs). Several PML isoforms (PMLI-PMLVII) derived from a single <i>PML</i> gene by alternative splicing, share the same N-terminal region but differ in their C-terminal sequences. Introducing each of the human PML isoform in PML-negative cells revealed that enhanced ...[more]

PMID: 29535160

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The SUMO protease SENP6 regulates the constitutive centromere-associated network by group

Project description:Project 1: Identification of SUMOylated proteins which are regulated by the SUMO protease SENP6. SENP6 knockdown was performed by two independent shRNAs and SUMOylated proteins were purified from U2OS expressing His10-tagged SUMO2 by means of Ni-NTA pulldown. Purified SUMOylated proteins were identified and quantified by label-free quantification. Project 2: Dynamics of chromatin-associated proteins influenced by SENP6. After siRNA-mediated knockdown of SENP6, chromatin fractions of U2OS cells were isolated and abundances of proteins were quantified. Project 3: Analysis of in vitro SUMOylated CENP-T for the presence of SUMOylated SUMO peptides. For this aim purified CENP-T-HA was in vitro SUMOylated with a SUMO Q87R mutant to reduce the length of the tryptic peptide and therefore to be able to identified sit-specific SUMOylation.

2019-09-13 | PXD011963 | Pride

Probing the Roles of SUMOylation in Cancer Cell Biology Using a Selective SAE inhibitor

Project description:Small ubiquitin-like modifier (SUMO) family proteins regulate target protein functions by post-translational modification. However, a potent and selective inhibitor to target the SUMO pathway has been lacking. Here we describe ML-792, the first mechanism-based SUMO-activating enzyme (SAE) inhibitor with nanomolar potency in cellular assays. ML-792 selectively blocks SAE enzyme activity and total SUMOylation, which leads to reduced cancer cell proliferation. Moreover, induction of the MYC oncogene increased the ML-792 mediated viability effect in cancer cells, indicating potential application of SAE inhibitors in MYC-amplified tumors. Using ML-792, we further explored the critical roles of SUMOylation in mitotic progression and chromosome segregation. Furthermore, expression of an SAE catalytic subunit (UBA2) mutant S95N/M97T rescued SUMOylation loss and the mitotic defect induced by ML-792, confirming the selectivity of ML-792. As a potent and selective SAE inhibitor, ML-792 provides rapid loss of endogenously SUMOylated proteins allowing for novel insights into SUMO biology.

2017-09-01 | GSE100408 | GEO

CP190 and CTCF mediated enhancer blocking is augmented by SUMOylation

Project description:Chromatin insulators shield promoters and chromatin domains from neighbouring enhancers or chromatin regions with opposing activities. Insulator binding proteins and their cofactors mediate the boundary function. In general, covalent modification of proteins by the Small Ubiqutin-like Modifier (SUMO) is an important mechanism to control the interaction of proteins within complexes. Here we addressed the impact of SUMO in respect to insulator function, chromatin binding of insulator factors and formation of insulator speckles. SUMOylation augments the enhancer blocking function of four different insulator sequences and increases the genome-wide binding of the insulator cofactor CP190. A model is discussed with enhanced chromatin binding of SUMOylated CP190 causing fusion of insulator speckles, which may allow for more efficient insulation.

2017-08-07 | GSE96581 | GEO

Extensive SUMO modification of chromatin factors distinguishes pluripotent from somatic cells

Project description:The post-translational modification of proteins by SUMO acts as a key gatekeeper of cell identity. In mouse embryonic fibroblast (MEFs), SUMO impedes reprogramming to pluripotency, while in embryonic stem cells (ESCs), it represses the emergence of totipotent-like cells, suggesting that SUMO targets distinct sets of substrates to preserve the somatic and pluripotent states. Using MS-based proteomics, we show here that the composition of the endogenous SUMOylomes differs dramatically between MEFs and ESCs. In MEFs, SUMOylated proteins organize in a rather diffuse functional network enriched in nuclear factors with general cellular functions. In contrast, in ESCs, SUMOylated proteins form a tightly interconnected network mainly composed of repressive chromatin complexes. We also characterized several SUMOylated pluripotency factors and show that SUMO modification of Dppa2 and Dppa4 hampers their ability to induce a totipotent-like state. Altogether, we propose that rewiring the repertoire of SUMO target networks is a major driver of cell fate transition during embryonic development.

2020-09-04 | GSE144881 | GEO

Is transthyretin a regulator of Ubc9 SUMOylation?

Project description:Ageing and mutations of transthyretin (TTR), the thyroid hormones and retinol transporting protein lead to amyloidosis by destabilizing the structure of TTR. Because protein structure is regulated through posttranslational modifications, we investigated the Small Ubiquitin-like Modifier (SUMO)ylation of TTR. We chose the widely used Ubc9 fusion-directed SUMOylation system, which is based on a fusion of the SUMOylation substrate of interest with Ubc9, a sole SUMO conjugating enzyme. Surprisingly, despite our presumptions, we found that Ubc9 fused to TTR was SUMOylated at a unique set of lysine residues. Three unknown SUMOylation sites of Ubc9—K154, K18 and K65—were revealed by mass spectrometry (MS). The previously reported SUMOylation at K49 of Ubc9 was also observed. SUMOylation of the lysine residues of TTR fused to Ubc9 was hardly detectable. However, non-fused TTR was SUMOylated via trans-SUMOylation by Ubc9 fused to TTR. Interestingly, mutating the catalytic residue of Ubc9 fused to TTR did not result in complete loss of the SUMOylation signal, suggesting that Ubc9 linked to TTR is directly cross-SUMOylated by the SUMO-activating enzyme E1. Ubc9, TTR or fusion proteins composed of TTR and Ubc9 specifically affected the global SUMOylation of cellular proteins. TTR or Ubc9 alone increased global SUMOylation, whereas TTR and Ubc9 together decreased the amount of high-molecular weight (HMW) SUMO conjugates. Our data suggest that TTR may influence the SUMOylation of Ubc9, thereby altering signalling pathways in the cell.

2016-08-15 | PXD004515 | Pride

Protein SUMOylation in the Drosophila ovary

Project description:Genome regulation involves complex and highly regulated protein interactions that are often mediated through post-translational modifications (PTMs). SUMOylation – the covalent attachment of the small ubiquitin-like modifier (SUMO) – is a conserved PTM in eukaryotes that has been implicated in a number of essential processes such as nuclear import, DNA damage repair, transcriptional control, and chromatin organization. In Drosophila, SUMO is essential for viability and its depletion from the female germline causes infertility associated with global loss of heterochromatin, and illicit upregulation of transposons and lineage-inappropriate genes. However, the specific targets of SUMO and its mechanistic role in different cellular pathways are still poorly understood. Here, we developed a proteomics-based strategy to characterize the SUMOylated proteome in Drosophila that allowed us to identify ~1500 SUMO sites in 843 proteins in the fly ovary. A high confidence set of SUMOylated proteins is highly enriched in factors involved in heterochromatin regulation and the piRNA pathway that represses transposons. Furthermore, SUMOylation of several piRNA pathway proteins occurs in a Piwi-dependent manner, indicating a functional implication of this modification in the cellular response to transposon activity. Together, these data highlight the impact of SUMOylation on epigenetic regulation and reveal an unexpectedly broad role of the SUMO pathway in the cellular defense against genomic parasites. Finally, this work provides a valuable resource and a system that can be adapted to the study of SUMOylation in other Drosophila tissues.

2023-04-17 | PXD037421 | Pride

Genome wide occupancy of SUMO machinery in proliferative and Ras-induced senescent human primary fibroblasts

Project description:Transcription factors represent one of the largest groups of proteins regulated by SUMO, and their modification has generally been correlated with transcriptional repression. However, as most of the studies focus on specific sumoylated transcriptional regulators, the distribution and global role of SUMO on chromatin in relation to transcription regulation remain largely unknown. To investigate this role, we determined the occupancy of SUMO machinery proteins on chromatin by ChIP coupled to sequencing in human primary cells. Examination of 3 histone modifications, Polymerase II, SUMO1, SUMO2, Ubc9 and PIASy in proliferative and Ras-induced senescent fibroblasts.

2013-07-24 | E-GEOD-42211 | biostudies-arrayexpress

Is transthyretin a regulator of Ubc9 SUMOylation?

2017-03-29 | MSV000080754 | MassIVE

Verticilium dahliae VdEno SUMOylation sites identify

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2023-08-01 | PXD043398 | Pride

Multifaceted down-regulation of the Srs2 helicase by the SUMO-like domain protein Esc2 promotes local recombination at sites of stalled replication

Project description:The SUMO-like domains-containing family of proteins to which Saccharomyces cerevisiae Esc2 belongs facilitates DNA damage tolerance (DDT) via elusive mechanisms. Here we report that Esc2 promotes recombination-mediated DDT by engaging in functional and physical interactions with Srs2 and Elg1, two readers of SUMOylated PCNA and modulators of DDT. These interactions depend on the SUMO Interacting Motifs of Elg1 and Srs2, and on the SUMO-like domains of Esc2. Mechanistically, Esc2 promotes Elg1 association to damaged and stalled forks and Srs2 turnover. Elg1 limits the levels of SUMOylated PCNA and subsequently of the anti-recombinase Srs2 at damaged sites, upholding local Rad51 binding. In conjunction with the SUMO–targeted ubiquitin ligase Slx5/Slx8, Esc2 also promotes proteasome-mediated Srs2 turnover, a process further enhanced by CDK-mediated Srs2 phosphorylation. Our results provide mechanistic insights into how SUMO- and DNA damage response-regulated pathways intersect to enable local error-free damage-bypass by recombination in the face of genotoxic stress. Proteins ChIP-chip analyses analysis were carried out as described (Bermejo et al., 2009). Labelled probes were hybridized to Affymetrix S.cerevisiae Tiling 1.0 (P/N 900645) arrays and processed with TAS software.

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