SubCellBarCode: Proteome-wide Mapping of Protein Localization and Relocalization

Orre, Lukas M.; Vesterlund, Mattias; Pan, Yifei; Arslan, Taner; Zhu, Yong; Fernandez-Woodbridge, Alejandro; Frings, Oliver; Fredlund, Erik; Lehtiö, Janne

doi:10.1016/j.molcel.2018.11.035

Cited by 168 publications

(236 citation statements)

References 41 publications

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“…Because proteins must at least partially co-localize to interact, we used subcellular fractionation profiles ('Subcell Bar Codes') for human proteins taken from a previously published study (Orre et al, 2019). Each protein in BioPlex 3.0 was matched with its subcellular fractionation profile.…”

Section: Subcellular Fractionation Correlation Among Bioplex Interactmentioning

confidence: 99%

“…P-value: Cramervon Mises test. (E) To assess the tendency for interacting proteins to co-localize, subcellular fractionation profiles (Orre et al 2019) were correlated for all interacting protein pairs in BioPlex. In tandem, we repeated the analysis for a randomized version of the BioPlex network.…”

Section: Additional Resourcesmentioning

confidence: 99%

“…Similarly, interacting proteins must co-localize. Comparison of subcellular Bar Codes (Orre et al, 2019) revealed that interacting proteins copurify upon subcellular fractionation (Figure S1E). Finally, we measured the assortativity of each GO SLIM category (Ashburner et al, 2000) in BioPlex relative to 1,000 randomized networks (Figure S1F).…”

Section: Introductionmentioning

confidence: 99%

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Dual Proteome-scale Networks Reveal Cell-specific Remodeling of the Human Interactome

Huttlin

Bruckner

Navarrete‐Perea

et al. 2020

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159

233

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SUMMARYThousands of interactions assemble proteins into modules that impart spatial and functional organization to the cellular proteome. Through affinity-purification mass spectrometry, we have created two proteome-scale, cell-line-specific interaction networks. The first, BioPlex 3.0, results from affinity purification of 10,128 human proteins – half the proteome – in 293T cells and includes 118,162 interactions among 14,586 proteins; the second results from 5,522 immunoprecipitations in HCT116 cells. These networks model the interactome at unprecedented scale, encoding protein function, localization, and complex membership. Their comparison validates thousands of interactions and reveals extensive customization of each network. While shared interactions reside in core complexes and involve essential proteins, cell-specific interactions bridge conserved complexes, likely ‘rewiring’ each cell’s interactome. Interactions are gained and lost in tandem among proteins of shared function as the proteome remodels to produce each cell’s phenotype. Viewable interactively online through BioPlexExplorer, these networks define principles of proteome organization and enable unknown protein characterization.

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Section: Subcellular Fractionation Correlation Among Bioplex Interactmentioning

confidence: 99%

Section: Additional Resourcesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Dual Proteome-scale Networks Reveal Cell-specific Remodeling of the Human Interactome

Huttlin

Bruckner

Navarrete‐Perea

et al. 2020

Preprint

159

233

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“…Compartmentalization is an essential characteristic of eukaryotic cells, ensuring that cellular processes are partitioned to defined subcellular locations. High throughput microscopy 1 and biochemical fractionation coupled with mass spectrometry [2][3][4][5][6] have helped to define the proteomes of multiple organelles and macromolecular structures. However, many compartments have remained refractory to such methods, partly due to lysis and purification artefacts and poor subcompartment resolution.…”

Section: Introductionmentioning

confidence: 99%

A proximity-dependent biotinylation map of a human cell: an interactive web resource

Knight

Rajasekharan

et al. 2019

Preprint

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INTRODUCTIONCompartmentalization is an essential characteristic of eukaryotic cells, ensuring that cellular processes are partitioned to defined subcellular locations. High throughput microscopy 1 and biochemical fractionation coupled with mass spectrometry 2-6 have helped to define the proteomes of multiple organelles and macromolecular structures. However, many compartments have remained refractory to such methods, partly due to lysis and purification artefacts and poor subcompartment resolution. Recently developed proximity-dependent biotinylation approaches such as BioID and APEX provide an alternative avenue for defining the composition of cellular compartments in living cells (e.g. 7-10 ). Here we report an extensive BioID-based proximity map of a human cell, comprising 192 markers from 32 different compartments that identifies 35,902 unique high confidence proximity interactions and localizes 4,145 proteins expressed in HEK293 cells. The recall of our localization predictions is on par with or better than previous large-scale mass spectrometry and microscopy approaches, but with higher localization specificity. In addition to assigning compartment and subcompartment localization for many previously unlocalized proteins, our data contain finegrained localization information that, for example, allowed us to identify proteins with novel roles in mitochondrial dynamics. As a community resource, we have created humancellmap.org, a website that allows exploration of our data in detail, and aids with the analysis of BioID experiments. BODYProximity-dependent labelling approaches have rapidly grown in popularity, as they provide a robust way to label the environment in which a protein resides in living cells 7,8 . In the most widely used of these techniques, BioID, a mutant E. coli biotin ligase -BirA* (R118G) -is fused in-frame with the coding sequence of a bait polypeptide of interest, and the resulting fusion protein expressed in cultured cells. While BirA* can activate biotin to biotinoyl-AMP, the abortive mutant enzyme exhibits a reduced affinity for the activated molecule. A reactive intermediate is thus released into the local environment that can react with free epsilon amine groups on nearby lysine residues 7 . This ability for BirA* to label a local environment has led to BioID being employed by multiple laboratories to define the composition, and in some cases the overall organization, of both membrane-bound and membraneless organelles (e.g. 7-10 ).Here, we set out to map a human cell by profiling markers (consisting of full-length proteins or targeting sequences) from 32 cellular compartments. These compartments include the cytosolic face of all membrane-bound organelles, the ER lumen, subcompartments of the nucleus and mitochondria, major membraneless organelles such as the centrosome and the nucleolus, and the main cytoskeletal structures (actin, microtubules and intermediate filaments). Several proteins were also queried throughout the endomembrane system to identify components enriched at locales a...

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“…This critical switch is controlled by EGFR ubiquitination [33,34]. We and others showed by antibody-based and antibody-free methods that UBTD1 is localized in various cell compartments including the plasma membrane, ER and vesicles [14,35]. Therefore, we first speculated that UBTD1 was implicated in EGFR cargoes internalization through ubiquitination of the receptor.…”

Section: Discussionmentioning

confidence: 98%

UBTD1 regulates ceramide balance and endolysosomal positioning to coordinate EGFR signaling

Torrino

Tiroille

Dolfi

et al. 2020

Preprint

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To adapt in an ever-changing environment, cells must integrate physical and chemical signals and translate them into biological meaningful information through complex signaling pathways. By combining lipidomic and proteomic approaches with functional analysis, we have shown that UBTD1 (Ubiquitin domain-containing protein 1) plays a crucial role in both the EGFR (Epidermal Growth Factor Receptor) self-phosphorylation and its lysosomal degradation. On the one hand, by modulating the cellular level of ceramides through ASAH1 (N-Acylsphingosine Amidohydrolase 1) ubiquitination, UBTD1 controls the ligand-independent phosphorylation of EGFR. On the other hand, UBTD1, via the ubiquitination of SQSTM1/p62 (Sequestosome 1) and endolysosome positioning, participates in the lysosomal degradation of EGFR. The coordination of these two ubiquitin-dependent processes contributes to the control of the duration of the EGFR signal. Moreover, we showed that UBTD1 depletion exacerbates EGFR signaling and induces cell proliferation emphasizing a hitherto unknown function of UBTD1 in EGF-driven cell proliferation. IntroductionAll living organisms perceive variations in their environment and translate them into intracellular signals via signaling pathways. In multicellular organisms, disturbances in this signal transduction mechanism induce inappropriate cell behavior and are associated with a plethora of diseases including cancer. Cellular signaling can be viewed as a finely tuned "space-time continuum" [1]. Receptors activated by their ligands at the plasma membrane are endocytosed, then moved along endocytic compartments to be routed to the lysosomes for final degradation or recycled back to the cell surface. Thus, the signal delivered to the cell is the sum of the signals emitted by the activated receptor at the plasma membrane and during its intracellular trafficking [2]. The responsiveness of these processes requires fast and accurate control in space and time, which is mainly ensured by post-translational modification (PTM) of proteins. Broadly, several aspects of cell signaling and receptor trafficking are regulated by proteolytic or non-proteolytic ubiquitination [2-6].Protein ubiquitination is a PTM that results in the covalent attachment of one or more ubiquitin to lysine residues of the substrate [7][8][9]. Ubiquitin conjugation occurs in a sequential three-step enzymatic process involving E1 (ubiquitin activation), E2 (ubiquitin conjugation), and E3 (ubiquitin ligation). In this hierarchical framework, there are only two E1s, over 30 E2s and hundreds of E3s in human, illustrating the large spectrum of E2s that contrasts with the high specificity of E3s in the recognition of substrates [10,11]. While the interaction of E3s with their substrates confers specificity to the system, E2s are more versatile and are commonly considered as "ubiquitin carriers" with an auxiliary rather than control role.However, the modulation of the functionality of E2/E3 complexes by scaffold proteins has been poorly investigated and few proteins ...

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SubCellBarCode: Proteome-wide Mapping of Protein Localization and Relocalization

Cited by 168 publications

References 41 publications

Dual Proteome-scale Networks Reveal Cell-specific Remodeling of the Human Interactome

Dual Proteome-scale Networks Reveal Cell-specific Remodeling of the Human Interactome

A proximity-dependent biotinylation map of a human cell: an interactive web resource

UBTD1 regulates ceramide balance and endolysosomal positioning to coordinate EGFR signaling

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