mitochondrial-derived compartment

cellstructuremech:mitochondrial_derived_compartment · Membrane organelle · Membrane bounded organelle · Proposed

An inducible compartment characterized in budding yeast that remodels the outer mitochondrial membrane into multilamellar domains, selectively concentrates membrane-associated proteins, and can enclose cytosolic material. [DOI:10.1083/jcb.202307035]

Image (not hosted — CC_BY_NC_SA_4_0): PMC11320809.1 fig1

Tom70/Tim50 fluorescence, MDC frequency and diameter plots, thin-section TEM and immunogold microscopy. Scale bars: A, 1 micrometer; D, 500 nanometers; E-I, 200 nanometers. OTHER · Saccharomyces cerevisiae (NCBITaxon:4932) · Zachary N. Wilson, Matt West, Alyssa M. English, Greg Odorizzi and Adam L. Hughes (2024), Figure 1, DOI 10.1083/jcb.202307035; CC BY-NC-SA 4.0. · CC_BY_NC_SA_4_0 · source: PMC PMC11320809.1 fig1 · DOI:10.1083/jcb.202307035

Synonyms: MDC

UniProt location names: UniProt Consortium, CC BY 4.0. Reference label and route sources.

Components

Component	Type	Part of / acts on	Grounding	Genes	Essential	Role
outer mitochondrial membrane-derived lipid bilayers	Lipid	part of	Reviewed label only (reviewed name; no accession asserted)			Membrane material remodeled into multilamellar domains. `DOI:10.1083/jcb.202307035` Results and electron tomography establish outer-membrane-derived multilamellar organization.
Mitochondrial outer membrane translocase complex, subunit Tom70	Protein	part of	`InterPro:IPR005687`	TOM70	UNKNOWN	Enriched membrane cargo and import receptor implicated in MDC biogenesis; not a claim that the entire TOM complex is enriched. `DOI:10.1083/jcb.202307035` Figure 1: fluorescence and immunogold microscopy identify Tom70-enriched multilamellar structures. `https://www.ebi.ac.uk/interpro/api/entry/interpro/protein/uniprot/P07213/?page_size=200` All integrated matches inspected on 2026-10-05; next=null. Sequence-family identity is distinct from compartment localization.
Tom71-type mitochondrial import receptor	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	TOM71	UNKNOWN	Selected membrane cargo detected in the yeast screen; no invariant abundance or stoichiometry is assigned. `DOI:10.7554/eLife.13943` Table 1 lists Tom71 among MDC cargo; Figure 7 tests Tom70/Tom71-dependent formation. `https://www.ebi.ac.uk/interpro/api/entry/interpro/protein/uniprot/P38825/?page_size=200` All integrated matches inspected on 2026-10-05; next=null. Sequence-family identity is distinct from compartment localization.
Dnm1-type mitochondrial fission GTPase	Protein	acts on	Reviewed label only (reviewed name; no accession asserted)	DNM1	DISPENSABLE	Peripheral fission machinery associated with MDC release, not required for initial compartment formation in the tested concanamycin A assay. `DOI:10.7554/eLife.13943` Figure 4 and Figure 4 supplement 1: dnm1 deletion prevents release while MDCs form; Dnm1-GFP foci occur near MDCs. `https://www.ebi.ac.uk/interpro/api/entry/interpro/protein/uniprot/P54861/?page_size=200` All integrated matches inspected on 2026-10-05; next=null. Sequence-family identity is distinct from compartment localization.
enclosed cytosolic material	Other	part of	Reviewed label only (reviewed name; no accession asserted)			Cytosolic material can be enclosed in a subset of MDCs; closure is not demonstrated for every observed structure. `DOI:10.1083/jcb.202307035` Cytosolic GFP-IAA7 capture and auxin-protection experiments support enclosure in a subset of MDCs.

Organism-specific protein examples

Named proteins in which each component's role was established, with the organism the evidence comes from. The component above is the taxon-agnostic family; these are the specific entries behind it.

Mitochondrial outer membrane translocase complex, subunit Tom70

Accession	Protein	Gene	Organism	Entry
`UniProtKB:P07213`	Mitochondrial import receptor subunit TOM70	TOM70	Saccharomyces cerevisiae S288C (`NCBITaxon:559292`)	REVIEWED
Role and evidence (2 references) Reviewed reference-sequence example for the yeast protein. `UniProtKB:P07213` Native reviewed entry verifies name, gene and reference taxon. `DOI:10.1083/jcb.202307035` Figure 1: fluorescence and immunogold microscopy identify Tom70-enriched multilamellar structures.

Tom71-type mitochondrial import receptor

Accession	Protein	Gene	Organism	Entry
`UniProtKB:P38825`	Protein TOM71	TOM71	Saccharomyces cerevisiae S288C (`NCBITaxon:559292`)	REVIEWED
Role and evidence (2 references) Reviewed reference-sequence example for the yeast protein. `UniProtKB:P38825` Native reviewed entry verifies name, gene and reference taxon. `DOI:10.7554/eLife.13943` Table 1 lists Tom71 among MDC cargo; Figure 7 tests Tom70/Tom71-dependent formation.

Dnm1-type mitochondrial fission GTPase

Accession	Protein	Gene	Organism	Entry
`UniProtKB:P54861`	Dynamin-related protein DNM1	DNM1	Saccharomyces cerevisiae S288C (`NCBITaxon:559292`)	REVIEWED
Role and evidence (2 references) Reviewed reference-sequence example for the yeast protein. `UniProtKB:P54861` Native reviewed entry verifies name, gene and reference taxon. `DOI:10.7554/eLife.13943` Figure 4 and Figure 4 supplement 1: dnm1 deletion prevents release while MDCs form; Dnm1-GFP foci occur near MDCs.

Canonical examples

NCBITaxon:4932 Saccharomyces cerevisiae — Experimentally characterized budding-yeast MDCs; no broad fungal or eukaryotic prevalence claim. [DOI:10.7554/eLife.13943]
NCBITaxon:559292 Saccharomyces cerevisiae S288C — Methods identify S288C (BY) derivatives for the imaging and perturbation experiments; reference accessions do not specify one unmodified experimental strain. [DOI:10.1083/jcb.202307035]

Functions

selective sequestration of outer mitochondrial membrane proteins — Concentrates selected membrane-associated cargo while excluding or de-enriching other mitochondrial proteins. Protection of enclosed cargo is partial and condition dependent.
- DOI:10.1083/jcb.202307036 The 2024 cargo study distinguishes surplus outer-membrane proteins from correctly localized inner-membrane carriers.
- DOI:10.1083/jcb.202307035 Membrane-cargo degron experiments show partial protection, not permanent isolation.
conditional routing of mitochondrial membrane cargo toward vacuolar degradation — An intermediate in Tom70-GFP delivery to the vacuole after concanamycin A treatment; release and downstream autophagic delivery are distinct from formation.
- DOI:10.7554/eLife.13943 Figure 4: fission-deficient and atg5 deletion cells still form MDCs but differ in subsequent release and vacuolar delivery. This is not a universal fate of all MDCs.

Physical properties

DIAMETER: 0.41 UO:0000017 (Mean diameter of 104 spherical rapamycin-induced MDCs in haploid budding yeast; 200 nM rapamycin for 2 hours.)
- DOI:10.1083/jcb.202307035 Figure 1C reports the mean in micrometers for spherical MDCs, as stated on the inspected plot axis. This does not measure elongated extensions or all MDC morphologies; TEM section thickness is not used as compartment diameter.
DIAMETER: 0.36 UO:0000017 (Mean diameter of 49 spherical concanamycin A-induced MDCs in haploid budding yeast; 500 nM concanamycin A for 2 hours.)
- DOI:10.1083/jcb.202307035 Figure S1C reports the mean in micrometers for spherical MDCs, as stated on the inspected plot axis. It is a separate condition, not a universal size range or a measurement of all MDC morphologies.

Mechanism graphs

Conditional MDC formation and release in budding yeast (ASSEMBLY)

Experimentally supported intervention effects and compartment capabilities.

Subject	Predicate	Object	Evidence
Rapamycin treatment (200 nM, 2 hours)	induces	MDC formation in budding yeast	`DOI:10.1083/jcb.202307035` Figure 1 and MDC-assay Methods: rapamycin induces Tom70-enriched, Tim50-depleted structures.
MDC formation in budding yeast	enables	Selective concentration of outer-membrane cargo	`DOI:10.1083/jcb.202307036` Results distinguish enriched selected outer-membrane proteins from non-enriched TOM and inner-membrane proteins.
MDC formation in budding yeast	enables	Enclosure of cytosolic material in a subset of MDCs	`DOI:10.1083/jcb.202307035` Cytosolic reporter/degron experiments support enclosure in a subset; not every MDC is shown to be closed.
Combined TOM70 and TOM71 deletion	impairs	MDC formation in budding yeast	`DOI:10.7554/eLife.13943` Figure 7: combined loss of Tom70 and Tom71 blocks formation in the tested assay.
MMM1 deletion	impairs	MDC formation in budding yeast	`DOI:10.1083/jcb.202002144` ERMES-deletion experiments impair formation under the tested induction conditions; later bypass experiments limit claims of absolute essentiality.
GEM1 deletion	impairs	MDC formation in budding yeast	`DOI:10.1083/jcb.202002144` Gem1-deletion experiments impair induction; the dependency is conditional, not evidence that Gem1 defines the compartment.
DNM1 deletion	impairs	MDC release from mitochondria during concanamycin A treatment	`DOI:10.7554/eLife.13943` Figure 4: initial formation persists but subsequent release is impaired.
PSD1 deletion	promotes	MDC formation in budding yeast	`DOI:10.1083/jcb.202302069` PE-biosynthesis perturbation promotes constitutive MDC formation in a subset of cells; this is not a prevalence estimate.
CRD1 deletion	reduces	MDC formation in budding yeast	`DOI:10.1083/jcb.202302069` CL-biosynthesis perturbation reduces formation without eliminating it from every cell.

Discussions

INTERPRETATION (RESOLVED): Keep the named MDC distinct from other mitochondrial deposits and vesicles. Outer-membrane remodeling and multilamellar topology define this record; the compartment is not just a protein aggregate or a generic mitochondrion-derived vesicle.
INTERPRETATION (RESOLVED): Use the revised outer-membrane cargo model. The 2016 carrier interpretation was revised after testing tag orientation, localization and function.
INTERPRETATION (RESOLVED): Separate observed cargo and release machinery from upstream regulators. Colocalization, genetic dependency, and membership in the compartment are different observations.
CURATION_TODO (OPEN): Resolve exact source-neutral identities for the label-only component classes. Heterogeneous membrane/cytosolic material has no single molecular identity; the inspected Tom71 and Dnm1 matches do not support exact family groundings.
CURATION_TODO (OPEN): Resolve differing lipid-perturbation phenotypes between studies. The 2020 study reports no formation defect for tested crd1/ups1/psd1 perturbations, whereas the dedicated 2024 lipid study detects distinct CL- and PE-pathway effects.
CURATION_TODO (OPEN): Reassess 2026 regulatory and adaptive-function models when full primary evidence and final versions are available. Two relevant 2026 bioRxiv studies have eLife reviewed-preprint versions; neither is treated here as a version of record or proof of MDC-specific fitness benefit.

Evidence

DOI:10.7554/eLife.13943 PMID 27097106, PMC4889329.1. Read Results on MDC formation, fission, cargo and Tom70/71, plus Discussion and associated captions; not all early aging Results or supplemental data.
DOI:10.1083/jcb.202307035 PMID 39136939, PMC11320809.1. Read all main Results, Discussion, selected strain/culture/imaging Methods and captions; actual Figure 1 inspected. Raw images and tomography were not reanalyzed. Figure S1 was additionally inspected during PR 2054 review; its native PMC media MD5 5b329e0ccfd3de22c02265e8439eda9f was verified.
DOI:10.1083/jcb.202307036 PMID 39136938, PMC11320589.1. Read Discussion and selected Results on cargo and carrier-reporter localization, with figure captions; not every supplementary experiment.
DOI:10.1083/jcb.202002144 PMID 33090183, PMC7588143.1. Read combined Results/Discussion and selected strain and MDC-assay Methods.
DOI:10.1083/jcb.202302069 PMID 38497895, PMC10949074.1. Read Discussion and Results on Ups proteins, CL and PE perturbations and bypass phenotypes; no raw lipidomics reanalysis.
GO:0043231 Native QuickGO verifies active cellular-component term intracellular membrane-bounded organelle as a broader parent, not exact MDC identity.

Curation history

2026-10-05T05:29:54Z codex · CREATED_RECORD — Scaffolded by scripts/new_record.py
2026-10-05T05:34:35Z codex · EXPANDED_RECORD — Added yeast-scoped MDC composition, revised cargo model, bounded intervention graph, measured dimensions, inspected link-only figure and explicitly limited 2026 preprint follow-up evidence.
2026-10-05T05:55:38Z codex · REFINED_MEASUREMENT_SCOPE — Addressed PR 2054 review issue 2055 by restricting both diameter contexts to the spherical MDCs sampled in Figure 1C and Figure S1C; preserved values, units, sample sizes and induction conditions.

Source: data/structures/membrane_organelle/mitochondrial_derived_compartment.yaml