TABLE 1:

Proteins that aggregate in Δyme1 mitochondria.

	Open reading frame	Protein	Submitochondrial locationa	Transmembrane domainsa	Cofactor	Functionb
1	Q0250	COX2	IM-IMS	2	Copper	Subunit II of cytochrome c oxidase, mitochondrially encoded
2	YAL039C	CYC3	IMS	—	Heme, iron	Cytochrome c heme lyase (holocytochrome c synthase), attaches heme to apo-cytochrome c in the IMS
3	YBL095W	—	Not known	1	—	Unknown
4	YBR262C	AIM5	IM-IMS	1	—	Subunit of mitochondrial IM organizing system (MitOS/MICOS/MINOS), role in maintenance of cristae junctions and IM architecture
5	YBR282W	MRPL27	Matrix	—	—	Mitochondrial ribosomal protein of the large subunit
6	YCL044C	MGR1	IM-IMS	2	—	Subunit of mitochondrial i-AAA protease, which degrades misfolded mitochondrial proteins, binds to substrates to facilitate proteolysis, and is required for growth of rho0 cells
7	YCR071C	IMG2	Matrix	—	—	Mitochondrial ribosomal protein of the large subunit
8	YDL174C	DLD1	IM-IMS	1	FAD, zinc	d-lactate dehydrogenase, oxidizes d-lactate to pyruvate
9	YDR316W	OMS1	IM-IMS	1	—	With conserved methyltransferase motif, multicopy suppressor of respiratory defects caused by OXA1 mutations
10	YFL036W	RPO41	Matrix	—	—	RNA polymerase; enhancing DNA bending and melting to facilitate preinitiation open-complex formation
11	YFR011C	AIM13	IMS	—	—	Subunit of mitochondrial IM organizing system (MitOS/MICOS/MINOS), role in maintenance of cristae junctions and IM architecture
12	YGL057C	GEP7	IM	1	—	Unknown function; null mutant exhibits respiratory growth defect and synthetic interactions with prohibitin (Phb1) and Gem1
13	YGL068W	MNP1	Matrix	—	—	Protein associated with mitochondrial nucleoid, required for normal respiratory growth
14	YGR029W	ERV1	IMS	—	FAD	Flavin-linked sulfhydryl oxidase, oxidizes Mia40p as part of the disulfide relay system
15	YGR076C	MRPL25	Matrix	—	—	Mitochondrial ribosomal protein of the large subunit
16	YGR132C	PHB1	IM-IMS	1	—	Inner mitochondrial membrane chaperone that stabilizes newly synthesized proteins
17	YGR174C	CBP4	IM-IMS	1	—	Required for assembly of cytochrome bc1 complex; interacts with the Cbp3-Cbp6 complex and newly synthesized cytochrome b to promote assembly of cytochrome b into cytochrome bc1 complex
18	YGR286C	BIO2	Matrix	—	Iron, sulfur	Biotin synthase, catalyzes the conversion of dethiobiotin to biotin
19	YHL021C	AIM17	Not known	—	Iron	Unknown; null mutant displays reduced frequency of mitochondrial genome loss
20	YHR005C-A	TIM10	IMS	—	Zinc	Essential IMS protein, forms a complex with Tim9 that delivers hydrophobic proteins to TIM22 complex for insertion into the IM
21	YHR024C	MAS2	Matrix	—	Zinc	Large subunit of mitochondrial processing protease, essential processing enzyme, cleaves the N-terminal targeting sequences from mitochondrially imported proteins
22	YIL155C	GUT2	IM-IMS	1	FAD	Mitochondrial glycerol-3-phosphate dehydrogenase
23	YJL066C	MPM1	Not known	—	—	Unknown function, no hydrophobic stretches
24	YJR045C	SSC1	Matrix	—	ATP	Hsp70 family ATPase, constituent of the import motor component of TIM23 complex, involved in protein translocation and folding
25	YJR048W	CYC1	IMS	—	Heme, iron	Electron carrier of mitochondrial intermembrane space, transfers electrons from ubiquinone-cytochrome c oxidoreductase to cytochrome c oxidase during cellular respiration
26	YJR100C	AIM25	Not known	—	—	Unknown function, null mutant viable/displays elevated rate of mitochondrial genome loss
27	YKL138C	MRPL31	Matrix	—	—	Mitochondrial ribosomal protein of the large subunit
28	YKL150W	MCR1	OM/IMS	1/-	FAD, NAD	Mitochondrial NADH-cytochrome b5 reductase, involved in ergosterol biosynthesis
29	YKR016W	FCJ1	IM-IMS	1	—	Orthologue of mammalian mitofilin, essential role in maintenance of cristae junctions and IM architecture, component of mitochondrial IM organizing system (MitOS/MICOS/MINOS)
30	YLL027W	ISA1	Matrix	—	—	Required for maturation of mitochondrial (4Fe-4S) proteins
31	YLR168C	UPS2	IMS	—	—	Role in regulation of phospholipid metabolism by inhibiting conversion of phosphatidylethanolamine to phosphatidylcholine
32	YLR203C	MSS51	Matrix	—	—	Translational activator for the mitochondrial COX1 mRNA; influences COX1 mRNA translation and Cox1 assembly into cytochrome c oxidase
33	YML025C	YML6	Matrix	—	—	Mitochondrial ribosomal protein of the large subunit
34	YMR115W	MGR3	IM-IMS	1	—	Subunit of mitochondrial i-AAA protease, which degrades misfolded mitochondrial proteins, binds to substrates to facilitate proteolysis, and is required for growth of rho0 cells
35	YMR145C	NDE1	IM-IMS	1	FAD, NAD	Mitochondrial external NADH dehydrogenase, catalyzes oxidation of cytosolic NADH, providing it to the respiratory chain
36	YMR203W	TOM40	OM-IMS	β-barrel	—	Component of the TOM complex, responsible for recognition and initial import steps for all mitochondrially directed proteins
37	YNL100W	AIM37	IM-IMS	2	—	Subunit of mitochondrial IM organizing system (MitOS/MICOS/MINOS), role in maintenance of cristae junctions and IM architecture
38	YNR018W	RCF2	IM-IMS	2	—	Cytochrome c oxidase subunit; role in assembly of respiratory supercomplexes; required for late-stage assembly of the Cox12 and Cox13 and for cytochrome c oxidase activity
39	YNR020C	ATP23	IMS	—	Zinc	Metalloprotease of the IM, required for processing of Atp6; role in assembly of the F0 sector of the F1F0 ATP synthase complex
40	YOR020C	HSP10	Matrix	—	—	Matrix cochaperonin that inhibits the ATPase activity of Hsp60; involved in protein folding and sorting in mitochondria; similarity to Escherichia coli groES
41	YOR211C	MGM1	IM-IMS/IMS	1/-	GTP	GTPase; complex with Ugo1 and Fzo1; required for mitochondrial morphology and genome maintenance; long and short form; homologue of human OPA1 involved in autosomal dominant optic atrophy

Wild-type and Δyme1 cells were grown in medium containing light or heavy lysine, mitochondria were isolated, and soluble and aggregate fractions were separated by centrifugation. Aggregate fractions were analyzed by MS. Four biological replicates were analyzed. The table contains alphabetically sorted mitochondrial proteins that showed at least 1.6-fold higher aggregation propensity in mitochondria lacking Yme1 in at least two of the experiments. Only proteins with at least two different quantified peptides were considered.

^aIM: inner membrane. OM: outer membrane. Submitochondrial localization and transmembrane domains according to the Uniprot database (www.uniprot.org).

^bFunction according to the Saccharomyces Genome Database (www.yeastgenome.org).