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PROTEOME: Quantitative SUMO proteomics reveals the modulation of several PML nuclear body associated proteins and an anti-senescence function of UBC9

ABSTRACT: Study the changes in the SUMO proteome during hRas enduced Senescence

INSTRUMENT(S): Orbitrap Fusion, LTQ Orbitrap Elite, Q Exactive

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

SUBMITTER: Pierre Thibault

PROVIDER: MSV000081600 | MassIVE | Tue Oct 10 12:42:00 BST 2017

SECONDARY ACCESSION(S): PXD007939

REPOSITORIES: MassIVE

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Quantitative SUMO proteomics reveals the modulation of several PML nuclear body associated proteins and an anti-senescence function of UBC9.

Project description:Several regulators of SUMOylation have been previously linked to senescence but most targets of this modification in senescent cells remain unidentified. Using a two-step purification of a modified SUMO3, we profiled the SUMO proteome of senescent cells in a site-specific manner. We identified 25 SUMO sites on 23 proteins that were significantly regulated during senescence. Of note, most of these proteins were PML nuclear body (PML-NB) associated, which correlates with the increased number and size of PML-NBs observed in senescent cells. Interestingly, the sole SUMO E2 enzyme, UBC9, was more SUMOylated during senescence on its Lys-49. Functional studies of a UBC9 mutant at Lys-49 showed a decreased association to PML-NBs and the loss of UBC9's ability to delay senescence. We thus propose both pro- and anti-senescence functions of protein SUMOylation.

| S-EPMC5958138 | biostudies-literature

SUMO-modified nuclear cyclin D1 bypasses Ras-induced senescence.

Project description:Oncogene-induced senescence represents a key tumor suppressive mechanism. Here, we show that Ras oncogene-induced senescence can be mediated by the recently identified haploinsufficient tumor suppressor apoptosis-stimulating protein of p53 (ASPP) 2 through a novel and p53/p19(Arf)/p21(waf1/cip1)-independent pathway. ASPP2 suppresses Ras-induced small ubiquitin-like modifier (SUMO)-modified nuclear cyclin D1 and inhibits retinoblastoma protein (Rb) phosphorylation. The lysine residue, K33, of cyclin D1 is a key site for this newly identified regulation. In agreement with the fact that its nuclear localization is required for its oncogenic activity, we show that nuclear cyclin D1 is far more potent than wild-type (WT) cyclin D1 in bypassing Ras-induced senescence. Thus, this study identifies SUMO modification as a positive regulator of nuclear cyclin D1, and reveals a new way by which cell cycle entry and senescence are regulated.

| S-EPMC3131893 | biostudies-literature

SUMO safeguards somatic and pluripotent cell identities by enforcing distinct chromatin states [SUMO-ChIP-seq]

Project description:Mouse embryonic fibroblasts (MEFs) were generated from Ubc9fl/- and Ubc9+/+ embryos (E13.5). MEFs were treated with tamoxifen for six days to cause CreERT2 activation, and induce Ubc9 floxed allele deletion. We determined the ChIP-seq profiles of SUMO-1 and SUMO-2 using chromatin of wild-type MEFs Ubc9+/+ and of the corresponding Ubc9 KO MEFs which are entirely depleted for sumoylation. The analysis revealed the nearly complete absence of genome-wide binding of SUMO-1 and SUMO-2 in Ubc9-/- MEFs, attesting for antibody specificities.

2018-10-24 | GSE115842 | GEO

Prolyl Isomerase PIN1 Modulates Oncogene Induced Senescence by Regulating PML-Nuclear Body Dynamics

Project description:Mammalian cells possess intrinsic mechanisms to prevent tumorigenesis upon deleterious mutations, including oncogene-induced senescence (OIS). The molecular mechanisms underlying OIS are, however, complex, and remain to be characterized. In this study, we analyzed the changes in the nuclear (phospho)proteome during the progression of OIS. Interestingly, we found that most of the phosphosites regulated during OIS were Prolyl Isomerase Pin1 targets. Our results show that Pin1 is a key regulator of several PML-NB proteins, specifically regulating several proteins upon oncogene activation. We have found that the constitutive PML-NB proteins are significantly regulated when PIN1 is depleted. Furthermore, we show that PIN1 knockdown promotes cell proliferation, while diminishing the senescence phenotype and hallmarks of senescence such as p21. Thus, our data provides preliminary evidence that PML-NB proteins are involved in regulating OIS via phosphorylation, and that the prolyl isomerase PIN1 acts as a tumor suppressor in response to oncogenic ER:RasG12V activation.

| MSV000090326 | MassIVE

SUMO protease and proteasome recruitment at the nuclear periphery differently affect replication dynamics at arrested forks.

Project description:Nuclear pores complexes (NPCs) are genome organizers, defining a particular nuclear compartment enriched for SUMO protease and proteasome activities, and act as docking sites for DNA repair. In fission yeast, the anchorage of perturbed replication forks to NPCs is an integral part of the recombination-dependent replication restart mechanism (RDR) that resumes DNA synthesis at terminally dysfunctional forks. By mapping DNA polymerase usage, we report that SUMO protease Ulp1-associated NPCs ensure efficient initiation of restarted DNA synthesis, whereas proteasome-associated NPCs sustain the speed of restarted DNA polymerase. In contrast to Ulp1, this last function occurs independently of SUMO chains formation. By analyzing the role of the nuclear basket, the nucleoplasmic extension of the NPC, we reveal that the activities of Ulp1 and the proteasome cannot compensate for each other and affect the dynamics of RDR in distinct ways. Our work probes the mechanisms by which the NPC environment ensures optimal RDR.

2023-11-13 | GSE247371 | GEO

Rhes, a striatal enriched protein, regulates SUMOylation of nuclear proteins and gene expression in a SUMO-dependent manner

Project description:Rhes, a multifunctional striatal protein, regulates nuclear proteins and gene expression via SUMO-mediated mechnisms.

2020-11-23 | GSE150990 | GEO

SUMO-chain-regulated proteasomal degradation timing exemplified in DNA replication initiation

Project description:Similar to ubiquitin, SUMO forms chains, but the identity of SUMO-chain-modified factors and the purpose of this modification remain largely unknown. Here, we identify budding yeast SUMO protease Ulp2, able to disassemble SUMO chains, as a DDK interactor enriched at replication origins that promotes DNA replication initiation. Replication-engaged DDK is SUMOylated on chromatin, becoming a degradation-prone substrate when Ulp2 no longer protects it against SUMO-chain assembly. Specifically, SUMO chains channel DDK for SUMO-targeted ubiquitin ligase Slx5/Slx8-mediated and Cdc48 segregase-assisted proteasomal degradation. Importantly, the SUMOylation-defective ddk-KR mutant rescues inefficient replication onset and MCM activation in cells lacking Ulp2, suggesting that SUMO chains time DDK degradation. Using two unbiased proteomic approaches, we further identify subunits of the MCM helicase and other factors as SUMO-chain-modified degradation-prone substrates of Ulp2 and Slx5/Slx8. We thus propose SUMO-chain-/Ulp2-protease-regulated proteasomal degradation as a mechanism that times the availability of functionally-engaged SUMO-modified protein pools during replication and beyond.

2019-09-10 | GSE113835 | GEO

AR function is altered by polyglutamine expansion and by SUMO

Project description:Expansion of a polyglutamine (polyQ) tract in the gene for the androgen receptor (AR) results in partial loss of transactivation function and causes spinobulbar muscular atrophy (SBMA). Modification of AR by small ubiquitin-like modifier (SUMO) reduces AR function in a promoter context-dependent manner. We used microarrays to confirm and demonstrate loss of AR function from polyQ expansion and to test the degree to which AR function is altered by preventing polyQ AR SUMOylation. PC12 cells expressing AR10Q, AR112Q, or nonSUMOylatable AR112Q (KRKR) in the presence or absence of synthetic androgen R1881 were assessed for alterations in AR function by comparing gene expression changes with each AR variant in response to ligand.

2014-08-23 | E-GEOD-50383 | biostudies-arrayexpress

AR function is altered by polyglutamine expansion and by SUMO

2014-08-23 | GSE50383 | GEO

Expression Data from Ectopic expression of SUMO-1 in C. elegans

Project description:Transgenic C. elegans strains that express human SUMO-1 under the control of pan-neuronal (aex-3) or pan muscular (myo-4) promoters were assayed for gene expression changes. Control N2 non transgenic worms were compared to aex-3::His-SUMO-1 and myo-4::His-SUMO-1 worms in 3 biological replicate populations

2011-01-31 | E-GEOD-19972 | biostudies-arrayexpress

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