MitoStore

cellstructuremech:mitostore · Inclusion · Inclusion body · Proposed

A transient cytosolic protein granule characterized in budding yeast that sequesters non-imported mitochondrial precursor proteins, is enriched for presequence-containing cargo and associates with the mitochondrial surface. [DOI:10.15252/embj.2022112309]

Mitochondrial precursor reporters and Hsp104-positive granules in yeast. A: Aim17, Pdb1 and Mam33 reporter localization in wild-type and rpn4-deletion cells with control or clogger expression. B: separate hsp104- and hsp42-deletion Aim17 assays. C: targeting-sequence-deleted Mam33. D: glucose/lactate growth conditions. Scale bars: A, 2 micrometers; B and D, 10 micrometers; C, 5 micrometers. FLUORESCENCE · *Saccharomyces cerevisiae* (`NCBITaxon:4932`) · Lena Krämer, Niko Dalheimer, Markus Räschle, Zuzana Storchová, Jan Pielage, Felix Boos, Johannes M Herrmann (2023), Figure 5; CC BY 4.0, via PubMed Central. Unmodified. · CC_BY_4_0 · source: PMC PMC10068336.1 embj2022112309-fig-0005 · `DOI:10.15252/embj.2022112309`

Synonyms: MitoStores

Part of: GO:0005737 — cytoplasm (no local record)

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
presequence-enriched protein precursor cargo	Other	part of	Reviewed label only (reviewed name; no accession asserted)		UNKNOWN	Non-imported proteins enriched for mitochondrial precursors with N-terminal targeting sequences. Membership depends on cargo and condition; some secretory precursors are also reported. `DOI:10.15252/embj.2022112309` Figures 3C and 4A-B compare Hsp104 pulldowns with DHFR controls. Figure 5A verifies Aim17, Pdb1 and Mam33 colocalization in specific conditions; enrichment is not an exhaustive constituent list.
Small heat shock protein	Protein	part of	`InterPro:IPR031107`	HSP42, HSP26	CONDITIONAL	Chaperone class represented by Hsp42 and Hsp26, whose stress-enriched co-purification supports candidate residence. Hsp42 is required for the tested Aim17-positive granules; the same requirement is not established for Hsp26. Neither fixed copy number nor identical functions are asserted. `DOI:10.15252/embj.2022112309` Figures 4C-D and Results identify Hsp26/Hsp42 enrichment in Hsp104 pulldowns under clogger stress and interpret them as MitoStore constituents; this is an association-based composition inference. `DOI:10.15252/embj.2022112309` Figures 5B and 6D support Hsp42-dependent reporter-granule formation in the tested yeast backgrounds, not a requirement for every member of the family. `InterPro:IPR031107` Native integrated family metadata and complete three-entry match sets for Q12329 and P15992 verify membership in this family. Domain IPR002068 and superfamily IPR008978 are not used as family identities.
Hsp104-type disaggregase	Protein	acts on	Reviewed label only (reviewed name; no accession asserted)	HSP104	CONDITIONAL	Chaperone bound to precursor-containing granules. HSP104 loss prevents the tested Aim17-positive granules, supporting a condition-specific formation requirement. It is not modeled as a fixed coat, nor does this experiment directly measure an Hsp104-mediated cargo-release step. `DOI:10.15252/embj.2022112309` Figure 5A shows colocalization with precursor reporters and Figure 5B separately tests hsp104 deletion; the actual Figure 5 panels were inspected. `https://www.ebi.ac.uk/interpro/api/entry/interpro/protein/uniprot/P31539/?page_size=200` All 11 integrated matches inspected, next=null; broader ClpA/B families are not substituted for the narrower component.

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.

Small heat shock protein

Accession	Protein	Gene	Organism	Entry
`UniProtKB:Q12329`	Heat shock protein 42	HSP42	Saccharomyces cerevisiae S288C (`NCBITaxon:559292`)	REVIEWED
Role and evidence (2 references) Reviewed reference-sequence example; not a reassignment of YPH499-derived experiments to S288C. Figures 4C-D support co-purification; Figures 5B and 6D show the Hsp42-loss granule phenotype. `UniProtKB:Q12329` Native reviewed entry verifies accession, recommended name, gene and taxon 559292. `DOI:10.15252/embj.2022112309` Figures 4C-D support co-purification; Figures 5B and 6D show the Hsp42-loss granule phenotype.
`UniProtKB:P15992`	Heat shock protein 26	HSP26	Saccharomyces cerevisiae S288C (`NCBITaxon:559292`)	REVIEWED
Role and evidence (2 references) Reviewed reference-sequence example; not a reassignment of YPH499-derived experiments to S288C. Figures 4C-D support clogger-dependent co-purification with Hsp104. Hsp26 essentiality and direct granule localization were not established here. `UniProtKB:P15992` Native reviewed entry verifies accession, recommended name, gene and taxon 559292. `DOI:10.15252/embj.2022112309` Figures 4C-D support clogger-dependent co-purification with Hsp104. Hsp26 essentiality and direct granule localization were not established here.

Hsp104-type disaggregase

Accession	Protein	Gene	Organism	Entry
`UniProtKB:P31539`	Heat shock protein 104	HSP104	Saccharomyces cerevisiae S288C (`NCBITaxon:559292`)	REVIEWED
Role and evidence (2 references) Reviewed reference-sequence example; not a reassignment of YPH499-derived experiments to S288C. Figures 3-5 show granule association, cargo co-purification and the HSP104-loss reporter-granule phenotype. `UniProtKB:P31539` Native reviewed entry verifies accession, recommended name, gene and taxon 559292. `DOI:10.15252/embj.2022112309` Figures 3-5 show granule association, cargo co-purification and the HSP104-loss reporter-granule phenotype.

Canonical examples

NCBITaxon:4932 Saccharomyces cerevisiae — The Methods state YPH499deltaarg4 derivatives unless otherwise specified. Native UniProt taxonomy lists YPH499 under species 4932; a bounded NCBI YPH499-name query yielded no separate strain taxid. The supplemental strain table was not independently inspected. [DOI:10.15252/embj.2022112309]
NCBITaxon:559292 Saccharomyces cerevisiae S288C — Reference-sequence provenance for the reviewed Hsp42, Hsp26 and Hsp104 examples. This is not the asserted background of the YPH499-derived imaging and perturbation experiments. [UniProtKB:Q12329]

Functions

temporary sequestration of non-imported precursor proteins — Concentrates a condition-dependent, presequence-enriched protein cargo in cytosolic granules near mitochondria when precursor supply exceeds import capacity.
- DOI:10.15252/embj.2022112309 Figures 3-5 establish the granules, cargo enrichment and condition-dependent reporter incorporation; Figure 6C/E-F supports mitochondrial-surface association.
retention of import-competent mitochondrial precursors — A pulse/chase split-GFP assay supports later mitochondrial access of Aim17 synthesized during import stress. This does not establish that every stored cargo is import competent, that all imported protein passed through a granule, or that an individual molecule was tracked directly from a granule into mitochondria.
- DOI:10.15252/embj.2022112309 Figure 6A-B and Results follow reporter redistribution and post-induction Aim17-GFP11 access to mitochondrial Oxa1-GFP1-10 after clogger expression stops.

Mechanism graphs

Condition-dependent precursor recruitment into MitoStores (ASSEMBLY)

Subject	Predicate	Object	Evidence
Expression of mitochondrial import clogger	promotes cytosolic accumulation of	Non-imported precursor protein cargo	`DOI:10.15252/embj.2022112309` Results in the Rpn4/proteome sections and Figures 2A, EV1A and 3C support precursor accumulation and Hsp104 association.
Non-imported precursor protein cargo	accumulates in	MitoStore	`DOI:10.15252/embj.2022112309` Figures 4A-B and 5A establish enrichment and Aim17/Pdb1/Mam33 reporter localization.
HSP42 deletion	impairs formation of	MitoStore	`DOI:10.15252/embj.2022112309` Figure 5B separately tests hsp42 deletion and Figure 6D tests Hsp104-GFP foci.
HSP104 deletion	impairs formation of	MitoStore	`DOI:10.15252/embj.2022112309` Figure 5B contains separate hsp104 and hsp42 deletion panels, not only a double-deletion experiment.
Removal of the Mam33 targeting sequence	impairs	Mam33 incorporation into granules	`DOI:10.15252/embj.2022112309` Figure 5C and its Results compare the truncated reporter with the intact-cargo observations.
Mam33 incorporation into granules	contributes reporter cargo to	MitoStore	`DOI:10.15252/embj.2022112309` Figure 5A demonstrates condition-specific localization; Figure 5C limits the targeting-sequence interpretation.

Reporter recovery and chaperone-dependent stress tolerance (FUNCTION)

Subject	Predicate	Object	Evidence
MitoStore	sequesters	Stored precursor cargo represented by Aim17	`DOI:10.15252/embj.2022112309` Figure 5A establishes Aim17-RFP localization with Hsp104.
Stored precursor cargo represented by Aim17	can remain competent for	Post-chase Aim17 access to mitochondria	`DOI:10.15252/embj.2022112309` Figure 6B measures Aim17-GFP11 complementation with mitochondrial Oxa1-GFP1-10 after induction and chase.
Stopping galactose-induced clogger expression	permits recovery of	Post-chase Aim17 access to mitochondria	`DOI:10.15252/embj.2022112309` Figure 6A-B and Results compare induction and the four-hour chase.
RPN4 deletion in the tested assays	increases the measured recovery of	Post-chase Aim17 access to mitochondria	`DOI:10.15252/embj.2022112309` Figure 6B compares wild-type and rpn4 deletion after clogger expression and recovery.
RPN4 deletion in the tested assays	increases	Viability during clogger stress	`DOI:10.15252/embj.2022112309` Figure 6G tests viability after 24-hour clogger exposure; the earlier Results distinguish this from cytosolic aggregation challenges.
HSP42 deletion in the rpn4 background	reduces	Viability during clogger stress	`DOI:10.15252/embj.2022112309` Figure 6G tests the relevant mutant backgrounds.
HSP104 deletion in the rpn4 background	reduces	Viability during clogger stress	`DOI:10.15252/embj.2022112309` Figure 6G tests the relevant mutant backgrounds.

Discussions

INTERPRETATION (RESOLVED): Keep the named precursor-rich cytosolic granule separate from other mitochondrial or protein deposits. Similarity, a shared chaperone marker and organelle proximity do not establish exact structure identity.
INTERPRETATION (RESOLVED): Retain the evidence difference between Hsp42 and Hsp26 within the shared small-HSP component class. A family-level component must not imply identical member requirements or direct localization evidence for every member.
CURATION_TODO (OPEN): Resolve exact Hsp104-family grounding and native cargo/resident inventories. Reporter enrichment and Hsp104 interactors are not a complete source-neutral composition model.
INTERPRETATION (RESOLVED): Do not import every Hsp104 interactor, regulator or mitochondrial-surface factor as a MitoStore component. General chaperone interactions and related aggregate assays may denote different structures.
INTERPRETATION (RESOLVED): Keep the import-chase and survival conclusions specific to their measured readouts. Chaperone perturbations are pleiotropic and a reporter chase does not track every stored molecule.
CURATION_TODO (OPEN): Reconcile the paper-linked PRIDE deposit's bibliography and processing metadata before using its raw-data inventory. The accession resolves but inconsistent metadata must not silently define composition or sample scope.
CURATION_TODO (OPEN): Resolve finer granule identity boundaries, experimental strain mappings, prevalence and material properties. One species and optical reporter assays do not establish universal prevalence, fixed dimensions or a liquid phase.

Datasets

Paper-linked Hsp104 AP-MS proteomics deposit (PXD035762) · PRIDE · PROTEOMICS
Organism: Saccharomyces cerevisiae
Native metadata inspected on 2026-10-05. Its references field names the Ubc8 paper with DOI 10.26508/LSA.202201526, while its processing narrative reports 2920 proteins and the MitoStore Hsp104 IP panel reports 1154. The publication field follows the MitoStore paper's own linkage. No sample count, full constituent inventory or corrected archive bibliography is inferred; raw files were not read.
- DOI:10.15252/embj.2022112309 The inspected Data availability statement explicitly cites PXD035762.
- https://www.ebi.ac.uk/pride/ws/archive/v2/projects/PXD035762 Native title and sample-processing description concern MitoStores/Hsp104 IP-MS; archive bibliographic and processing metadata conflict with that linkage.

Evidence

DOI:10.15252/embj.2022112309 Primary definition, precursor/chaperone association, reporter interventions, recovery assay and imaging.
DOI:10.1073/pnas.2300475120 Comparative boundary source: Tom70-associated heat-stress aggregates share features with MitoStores, but its experiments do not establish exact identity for every aggregate.

Curation history

2026-10-05T08:21:01Z codex · CREATED_RECORD — Scaffolded by scripts/new_record.py
2026-10-05T08:25:34Z codex · EXPANDED_RECORD — Added source-bounded MitoStore composition, family/reference grounding, precursor recruitment and recovery graphs, dataset-conflict provenance, and an inspected CC BY 4.0 primary figure.

Source: data/structures/inclusion/mitostore.yaml