Identification of proximal SUMO-dependent interactors using SUMO-ID

Barroso-Gomila, Orhi; Trulsson, Fredrik; Muratore, Veronica; Canosa, Iñigo; Merino-Cacho, Laura; Cortázar, Ana R.; Pérez, Coralia; Azkargorta, Mikel; Iloro, Ibón; Carracedo, Arkaitz; Aransay, Ana M.; Elortza, Félix; Mayor, Ugo; Vertegaal, Alfred C.O.; Barrio, Rosa; Sutherland, James D.

doi:10.1038/s41467-021-26807-6

Cited by 38 publications

(40 citation statements)

References 86 publications

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“…These biotinylated proteins can be enriched by affinity purification and identified by MS analysis, where the labeled proteins can be potential E3 substrate targets [ 171 ]. Recently, this approach has been updated for the identification of SUMO-dependent interactors [ 172 ]. In this strategy, TurboID (upgraded version of BioID) was split in two, one fragment was fused to SUMO and the complementary fragment to a protein of interest.…”

Section: Proteomics For Substrate Identificationmentioning

confidence: 99%

Insights in Post-Translational Modifications: Ubiquitin and SUMO

Salas-Lloret

González-Prieto

2022

IJMS

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Both ubiquitination and SUMOylation are dynamic post-translational modifications that regulate thousands of target proteins to control virtually every cellular process. Unfortunately, the detailed mechanisms of how all these cellular processes are regulated by both modifications remain unclear. Target proteins can be modified by one or several moieties, giving rise to polymers of different morphology. The conjugation cascades of both modifications comprise a few activating and conjugating enzymes but close to thousands of ligating enzymes (E3s) in the case of ubiquitination. As a result, these E3s give substrate specificity and can form polymers on a target protein. Polymers can be quickly modified forming branches or cleaving chains leading the target protein to its cellular fate. The recent development of mass spectrometry(MS) -based approaches has increased the understanding of ubiquitination and SUMOylation by finding essential modified targets in particular signaling pathways. Here, we perform a concise overview comprising from the basic mechanisms of both ubiquitination and SUMOylation to recent MS-based approaches aimed to find specific targets for particular E3 enzymes.

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Section: Proteomics For Substrate Identificationmentioning

confidence: 99%

Insights in Post-Translational Modifications: Ubiquitin and SUMO

Salas-Lloret

González-Prieto

2022

IJMS

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“…Thus PML NBs are implicated in a variety of key cell survival pathways, including the DNA damage response, senescence, gene expression regulation, apoptosis, nuclear proteolysis and the antiviral response (Pearson and Pelicci, 2001;Bischof et al, 2002;Dellaire and Bazett-Jones, 2004;Dellaire et al, 2006a;Villagra et al, 2006;Bernardi et al, 2008;Attwood et al, 2020). In addition, many components of the small-ubiquitin like modifier (SUMO) machinery, such as SUMO proteases (i.e., SENPs) and SUMO ligases (i.e., UBC9, PIAS), associate with PML NBs making these structures hubs for SUMO biology within the cell (Van Damme et al, 2010;Hattersley et al, 2011;Sahin et al, 2014;Brown et al, 2016;Barroso-Gomila et al, 2021). PML NBs range in diameter from 0.1 to 1 μm, with mammalian cells hosting 4-30 bodies (Table 1) (Banani et al, 2016;Hoischen et al, 2018).…”

Section: Structure and Function Of Promyelocytic Leukemia-associated Sub-cellular Domains And Lipid-associated Pml Structures The Structumentioning

confidence: 99%

Running ‘LAPS’ Around nLD: Nuclear Lipid Droplet Form and Function

McPhee

Salsman

Foster

et al. 2022

Front. Cell Dev. Biol.

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The nucleus harbours numerous protein subdomains and condensates that regulate chromatin organization, gene expression and genomic stress. A novel nuclear subdomain that is formed following exposure of cells to excess fatty acids is the nuclear lipid droplet (nLD), which is composed of a neutral lipid core surrounded by a phospholipid monolayer and associated regulatory and lipid biosynthetic enzymes. While structurally resembling cytoplasmic LDs, nLDs are formed by distinct but poorly understood mechanisms that involve the emergence of lipid droplets from the lumen of the nucleoplasmic reticulum and de novo lipid synthesis. Luminal lipid droplets that emerge into the nucleoplasm do so at regions of the inner nuclear membrane that become enriched in promyelocytic leukemia (PML) protein. The resulting nLDs that retain PML on their surface are termed lipid-associated PML structures (LAPS), and are distinct from canonical PML nuclear bodies (NB) as they lack key proteins and modifications associated with these NBs. PML is a key regulator of nuclear signaling events and PML NBs are sites of gene regulation and post-translational modification of transcription factors. Therefore, the subfraction of nLDs that form LAPS could regulate lipid stress responses through their recruitment and retention of the PML protein. Both nLDs and LAPS have lipid biosynthetic enzymes on their surface suggesting they are active sites for nuclear phospholipid and triacylglycerol synthesis as well as global lipid regulation. In this review we have summarized the current understanding of nLD and LAPS biogenesis in different cell types, their structure and composition relative to other PML-associated cellular structures, and their role in coordinating a nuclear response to cellular overload of fatty acids.

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“…These methods have also been used to detect extracellular protein-protein interactions between cells (Martell et al, 2016), intracellular homodimers (De Munter et al, 2017;Xue et al, 2017), and protein complexes (Schopp et al, 2017). The highly active enzyme TurboID was also recently split, allowing the investigation of organelle contact sites and SUMO-dependent interactions (Cho et al, 2020;Barroso-Gomila et al, 2021).…”

Section: Organelle Mapping With Proximity-dependent Biotinylation: Cu...mentioning

confidence: 99%

Proximity-Dependent Biotinylation Approaches to Explore the Dynamic Compartmentalized Proteome

Dionne

Gingras

2022

Front. Mol. Biosci.

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In recent years, proximity-dependent biotinylation approaches, including BioID, APEX, and their derivatives, have been widely used to define the compositions of organelles and other structures in cultured cells and model organisms. The associations between specific proteins and given compartments are regulated by several post-translational modifications (PTMs); however, these effects have not been systematically investigated using proximity proteomics. Here, we discuss the progress made in this field and how proximity-dependent biotinylation strategies could elucidate the contributions of PTMs, such as phosphorylation, to the compartmentalization of proteins.

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Identification of proximal SUMO-dependent interactors using SUMO-ID

Cited by 38 publications

References 86 publications

Insights in Post-Translational Modifications: Ubiquitin and SUMO

Insights in Post-Translational Modifications: Ubiquitin and SUMO

Running ‘LAPS’ Around nLD: Nuclear Lipid Droplet Form and Function

Proximity-Dependent Biotinylation Approaches to Explore the Dynamic Compartmentalized Proteome

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