A proximity-dependent biotinylation map of a human cell

Go, Christopher D.; Knight, James D.R.; Rajasekharan, Archita; Rathod, Bhavisha; Hesketh, Geoffrey G.; Abe, Kento T.; Youn, Ji‐Young; Samavarchi-Tehrani, Payman; Zhang, Hui; Zhu, Licheng; Popiel, Evelyn; Lambert, Jean‐Philippe; Coyaud, Étienne; Cheung, Sally W.T.; Rajendran, Dushyandi; Wong, Cassandra; Antonická, Hana; Pelletier, Laurence; Palazzo, Alexander F.; Shoubridge, Eric A.; Raught, Brian; Gingras, Anne‐Claude

doi:10.1038/s41586-021-03592-2

Cited by 349 publications

(382 citation statements)

References 61 publications

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“…Comparison between the two studies yielded 960 proteins unique to the current study, 536 unique to the TAP-MS study, and 159 proteins shared between the two (S3 Fig) . GO-term analysis for molecular function, biological process, and cellular component were performed on the hits from the TAP-MS data (S4, S5, and S6 Figs). Proximity labeling methods are particularly suited for identifying the location of bait proteins [23,24] therefore, cell component analysis was compared between the two lists (S7 Fig) . Given the high amount of unique hits, it was not surprising to see major differences between cell component enrichment between viral proteins. NSP1 uniquely enriched for hits associated with preinitiation complex and ribosomal components by BIOID, but not by TAP-MS. Contrastingly, NSP9 enriched for similar factors only by TAP-MS.…”

Section: Plos Pathogensmentioning

confidence: 99%

The proximal proteome of 17 SARS-CoV-2 proteins links to disrupted antiviral signaling and host translation

et al. 2021

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Viral proteins localize within subcellular compartments to subvert host machinery and promote pathogenesis. To study SARS-CoV-2 biology, we generated an atlas of 2422 human proteins vicinal to 17 SARS-CoV-2 viral proteins using proximity proteomics. This identified viral proteins at specific intracellular locations, such as association of accessary proteins with intracellular membranes, and projected SARS-CoV-2 impacts on innate immune signaling, ER-Golgi transport, and protein translation. It identified viral protein adjacency to specific host proteins whose regulatory variants are linked to COVID-19 severity, including the TRIM4 interferon signaling regulator which was found proximal to the SARS-CoV-2 M protein. Viral NSP1 protein adjacency to the EIF3 complex was associated with inhibited host protein translation whereas ORF6 localization with MAVS was associated with inhibited RIG-I 2CARD-mediated IFNB1 promoter activation. Quantitative proteomics identified candidate host targets for the NSP5 protease, with specific functional cleavage sequences in host proteins CWC22 and FANCD2. This data resource identifies host factors proximal to viral proteins in living human cells and nominates pathogenic mechanisms employed by SARS-CoV-2.

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Section: Plos Pathogensmentioning

confidence: 99%

The proximal proteome of 17 SARS-CoV-2 proteins links to disrupted antiviral signaling and host translation

et al. 2021

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“…A strong negative expression correlation was observed between genes in these categories and SERBP1 both in brain and patient-derived GBM samples, implicating SERBP1 in brain function and development (Kosti et al, 2020). Two proximity-dependent biotinylating screening studies identified SERBP1 as an interaction partner of RBPs known to regulate synaptic plasticity such as FMR1, FXR1, FXR2, CAPRIN1, and SYNCRIP (Youn et al, 2018;Go et al, 2021). Additionally, SERBP1 has a role in the SUMOylation of certain proteins (Lemos and Kobarg, 2006), and is itself SUMOylated (Hendriks et al, 2014) on a lysine-rich sequence between the two RGG boxes.…”

Section: Introductionmentioning

confidence: 99%

Structural Characterization of the RNA-Binding Protein SERBP1 Reveals Intrinsic Disorder and Atypical RNA Binding Modes

Baudin

Moreno-Romero

et al. 2021

Front. Mol. Biosci.

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RNA binding proteins (RBPs) are essential for critical biological processes such as translation regulation and mRNA processing, and misfunctions of these proteins are associated with diseases such as cancer and neurodegeneration. SERBP1 (SERPINE1 mRNA Binding Protein 1) is an RBP that comprises two RG/RGG repeat regions yet lacks other recognizable RNA-binding motifs. It is involved in mRNA maturation, and translational regulation. It was initially identified as a hyaluronic acid binding protein, but recent studies have identified central roles for SERBP1 in brain function and development, especially neurogenesis and synaptogenesis. SERBP1 regulates One-carbon metabolism and epigenetic modification of histones, and increased SERBP1 expression in cancers such as leukemia, ovarian, prostate, liver and glioblastoma is correlated with poor patient outcomes. Despite these important regulatory roles for SERBP1, little is known about its structural and dynamic properties, nor about the molecular mechanisms governing its interaction with mRNA. Here, we define SERBP1 as an intrinsically disordered protein, containing highly conserved elements that were shown to be functionally important. The RNA binding activity of SERBP1 was explored using solution NMR and other biophysical techniques. The outcome of these experiments revealed that SERBP1 preferentially samples compact conformations including a central, stable α-helix and show that SERBP1 recognizes G-rich RNA sequences at the C-terminus involving the RGG box and neighboring residues. Despite the role in RNA recognition, the RGG boxes do not seem to stabilize the central helix and the central helix does not participate in RNA binding. Further, SERBP1 undergoes liquid-liquid phase separation, mediated by salt and RNA, and both RGG boxes are necessary for the efficient formation of condensed phases. Together, these results provide a foundation for understanding the molecular mechanisms of SERBP1 functions in physiological and pathological processes.

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“…Of note, Liu and coworkers ( 16 ) detected multiple cross-links between AIFM1 and AK2 as well in mouse heart mitochondria. Moreover, charting large affinity purifications MS (AP-MS) depositories, we found that they contained multiple instances of COX subunits interacting with AIFM1 ( 30 – 32 ) ( Dataset S2 ). Yet, buried in datasets generated by large-scale analyses of the mitochondrial interactome, these indications for AIFM1 binding to COX seem to have gone unnoticed so far.…”

Section: Resultsmentioning

confidence: 99%

Molecular characterization of a complex of apoptosis-inducing factor 1 with cytochrome c oxidase of the mitochondrial respiratory chain

Hevler

Chiozzi

Cabrera‐Orefice

et al. 2021

Proc. Natl. Acad. Sci. U.S.A.

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Combining mass spectrometry–based chemical cross-linking and complexome profiling, we analyzed the interactome of heart mitochondria. We focused on complexes of oxidative phosphorylation and found that dimeric apoptosis-inducing factor 1 (AIFM1) forms a defined complex with ∼10% of monomeric cytochrome c oxidase (COX) but hardly interacts with respiratory chain supercomplexes. Multiple AIFM1 intercross-links engaging six different COX subunits provided structural restraints to build a detailed atomic model of the COX-AIFM12 complex (PDBDEV_00000092). An application of two complementary proteomic approaches thus provided unexpected insight into the macromolecular organization of the mitochondrial complexome. Our structural model excludes direct electron transfer between AIFM1 and COX. Notably, however, the binding site of cytochrome c remains accessible, allowing formation of a ternary complex. The discovery of the previously overlooked COX-AIFM12 complex and clues provided by the structural model hint at potential roles of AIFM1 in oxidative phosphorylation biogenesis and in programmed cell death.

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A proximity-dependent biotinylation map of a human cell

Cited by 349 publications

References 61 publications

The proximal proteome of 17 SARS-CoV-2 proteins links to disrupted antiviral signaling and host translation

The proximal proteome of 17 SARS-CoV-2 proteins links to disrupted antiviral signaling and host translation

Structural Characterization of the RNA-Binding Protein SERBP1 Reveals Intrinsic Disorder and Atypical RNA Binding Modes

Molecular characterization of a complex of apoptosis-inducing factor 1 with cytochrome c oxidase of the mitochondrial respiratory chain

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