Protein trafficking
Mapping the faces of mitochondria and ER
Open access · cc by · source: Europe PMC
APEX2 proximity biotinylation yields high-quality proteomic maps of cytosol-facing outer mitochondrial and ER membranes in living human cells.
Study at a glance
- Design
- Animal / in-vitro — APEX2 proximity labeling of cytosol-facing OMM and ER membranes in living HEK 293T cells
- N
- SILAC proteomic maps with two replicates per membrane — cell-resource study
- Population
- HEK 293T cells expressing OMM/ERM APEX2 fusions
- Outcome
- Proteomes of cytosol-facing outer mitochondrial and ER membranes
Structured fields used in claim comparison tables when every cited study has a complete layer.
Key findings
Maps capture expected functional classes and enrich many additional proteins (22 OMM; 72 ERM), providing resources beyond classical fractionation.
Methodology
Used APEX2 proximity labeling in living cells to define proteins on the OMM and ER membrane facing the cytosol.
Limitations
A proteomic inventory is not a full functional validation of every newly enriched protein.
How this study connects
Role on claims
Each row is a claim on a concept or method page where this paper supports, challenges, or qualifies the statement. Roles are hand-checked — not a model guess.
Three papers in this method list barely use knockout or knockdown. APEX2 proximity labelling mapped 22 outer-mitochondrial and 72 ER-membrane proteins facing the cytosol; scRNA-seq of H1 hESC progenitors found that 1.5% O2 increases CXCR4+ definitive-endoderm-like cells; caveolar-coat work purified caveolin–cavin complexes. Those are maps and culture conditions, not gene deletions.
Evidence for the claim as stated.
Lexicon hits also disagree with the genuine KO/KD set. APEX2 inventories, hESC scRNA-seq under hypoxia, and caveolar stoichiometry do not perturb named genes, so they cannot be cited as knockdown evidence for trafficking proteins they merely list.
Evidence for the claim as stated.
Not every tagged paper is a western-first study. APEX2 maps (22 OMM, 72 ERM proteins) are mass-spectrometry inventories; Wnt5a work uses purified ligand and receptor context to turn β-catenin–TCF signalling on or off; Cas13a plant antiviral work measures GFP and viral accumulation after targeting TuMV regions. Blots may appear as supporting assays, not as the experimental core.
Evidence for the claim as stated.
APEX2, Wnt5a, and Cas13a illustrate false-positive or peripheral lexicon hits: proximity proteomics, ligand/receptor signalling, and CRISPR interference on an RNA virus. Citing them as if they were western-blot method papers overstates how the method was used.
Evidence for the claim as stated.
Many papers in the CRISPR index mention CRISPR or Cas proteins in passing while the actual experiment is something else (APEX2 proximity labelling, pan-genome presence/absence, ChIP-seq of histone acylations, scRNA-seq of endoderm). Those hits show why a body-count lexicon over-recruits; they are not additional editing results.
Evidence for the claim as stated.
Several confocal-tagged papers use imaging only as a supporting localisation. APEX2 defined 22 OMM and 72 ERM cytosol-facing proteins by mass spectrometry; caveolar-coat work is biochemical stoichiometry plus ultrastructure (caveolin–cavin complex excluding EHD2/pacsin 2); N and TMV p50 were cytoplasmic in N. benthamiana with TIR-dependent association and HR in two days. Those localisation notes are not confocal trafficking movies.
Evidence for the claim as stated.
APEX2, caveolar ultrastructure, and plant TIR–p50 association are weaker confocal examples: proximity biotinylation, electron-microscopy-scale coat structure, and cytoplasmic HR biochemistry. Citing them as confocal method papers overstates the imaging.
Evidence for the claim as stated.
APEX2 proximity labelling in living cells defined cytosol-facing proteomes of the outer mitochondrial membrane and the ER membrane: expected functional classes plus many additions (22 OMM proteins; 72 ERM proteins), beyond classical fractionation. The inventory is not a full functional validation of every newly enriched protein.
Evidence for the claim as stated.
Genuine MS designs still disagree about what is being counted. APEX2 inventories membrane-face neighbours in living cells (22 OMM; 72 ERM); caveolar work quantifies a purified coat; Rab5 work maps three ubiquitin lysines; rice work maps histone acylations under stress. A 'proteomics paper' can be spatial, stoichiometric, or epigenetic, and those outputs are not interchangeable.
Evidence for the claim as stated.
APEX2 proximity maps of cytosol-facing OMM (22 proteins) and ERM (72 proteins) are mass-spectrometry inventories that may use EM only to confirm organelle context. The headline result is enrichment beyond classical fractionation, not an ultrastructural atlas of every new protein.
Evidence for the claim as stated.
Only the caveolar paper is clearly an ultrastructure-of-a-coat study. GPCR work compares 142 inactive and 27 active deposited structures; APEX2 is proteomics; salmon work is a 30-day transcriptome of fat-cell differentiation; Bt OMV uptake is live light-microscopy trafficking. Calling all five 'electron microscopy papers' overstates shared methods.
Evidence for the claim as stated.
Open questions
Tensions this paper is part of
From concept pages' “where studies disagree.” Disagreement means the same question; scope means different assays, populations, or outcomes.
Lexicon hits also disagree with the genuine KO/KD set. APEX2 inventories, hESC scRNA-seq under hypoxia, and caveolar stoichiometry do not perturb named genes, so they cannot be cited as knockdown evidence for trafficking proteins they merely list.
APEX2, Wnt5a, and Cas13a illustrate false-positive or peripheral lexicon hits: proximity proteomics, ligand/receptor signalling, and CRISPR interference on an RNA virus. Citing them as if they were western-blot method papers overstates how the method was used.
APEX2, caveolar ultrastructure, and plant TIR–p50 association are weaker confocal examples: proximity biotinylation, electron-microscopy-scale coat structure, and cytoplasmic HR biochemistry. Citing them as confocal method papers overstates the imaging.
- Supports · What proteins build the caveolar coat?
- Supports · Plant TIR domain binds viral elicitor
Genuine MS designs still disagree about what is being counted. APEX2 inventories membrane-face neighbours in living cells (22 OMM; 72 ERM); caveolar work quantifies a purified coat; Rab5 work maps three ubiquitin lysines; rice work maps histone acylations under stress. A 'proteomics paper' can be spatial, stoichiometric, or epigenetic, and those outputs are not interchangeable.
- Supports · What proteins build the caveolar coat?
- Supports · How does monoubiquitin turn down Rab5?
- Supports · Histone acylations respond to plant stress
Only the caveolar paper is clearly an ultrastructure-of-a-coat study. GPCR work compares 142 inactive and 27 active deposited structures; APEX2 is proteomics; salmon work is a 30-day transcriptome of fat-cell differentiation; Bt OMV uptake is live light-microscopy trafficking. Calling all five 'electron microscopy papers' overstates shared methods.
- Supports · What proteins build the caveolar coat?
- Supports · Shared class A GPCR activation path
- Supports · Salmon fat-cell differentiation transcriptome
- Supports · How do gut-bacteria vesicles enter host cells?
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