Table 1 Proteins co-purifying with HsCLPP^WT-TAG and HsCLPP^TRAP-TAG.

From: Identification of potential mitochondrial CLPXP protease interactors and substrates suggests its central role in energy metabolism

P. anserina ID*	Avg. Number of Unique Peptides HsCLPP^WT-TAG	Avg. Number of Unique Peptides HsCLPP^TRAP-TAG	Swiss-Prot ID	Gene	Protein
Chaperones and Protein Import
Pa_6_2570	27.0	28.3	P38646	HSPA9	Stress-70 protein‡
Pa_6_5750	16.7	13.7	P10809	HSPD1	60 kDa heat shock protein‡
Pa_2_9700	14.3	15.3	O94826	TOMM70A	Mitochondrial import receptor subunit TOM70
Pa_2_10580	9.0	9.3	O96008	TOMM40	Mitochondrial import receptor subunit TOM40
Pa_6_1920	3.0	2.7	Q15388	TOMM20	Mitochondrial import receptor subunit TOM20
Pa_2_12760	1.7	1.3	P35232	PHB	Prohibitin
Metabolism
Pa_1_22300	12.0	15.3	P23378	GLDC	Glycine cleavage system P protein
Pa_3_10790	11.3	13.0	O95571	ETHE1	Persulfide dioxygenase ETHE1
Pa_5_5970	10.0	9.0	Q99798	ACO2	Aconitate hydratase‡,§
Pa_3_11290	8.7	9.3	P00505	GOT2	Aspartate aminotransferase
Pa_6_1590	8.0	7.0	P24752	ACAT1	Acetyl-CoA acetyltransferase
Pa_3_6780	7.3	14.0	O75390	CS	Citrate synthase
Pa_6_2730	7.3	6.3	P50213	IDH3A	Isocitrate dehydrogenase [NAD] subunit alpha
Pa_3_2310	6.7	12.0	P10515	DLAT	Pyruvate dehydrogenase E2 component‡
Pa_5_11920	5.7	5.0	Q13825	AUH	Methylglutaconyl-CoA hydratase
Pa_2_1050	5.7	4.3	P78827†	ilv-2	Ketol-acid reductoisomerase
Pa_6_10000	5.0	3.7	C7C436†	mcsA	2-methylcitrate synthase
Pa_1_13140	4.7	6.3	P31327	CPS1	Carbamoyl-phosphate synthetase I‡ (Pa_1_13140 matches to large chain/C-terminal region)
Pa_3_7700	4.3	7.7	Q9P2R7	SUCLA2	Succinyl-CoA ligase subunit beta‡
Pa_1_3450	4.0	6.0	Q92506	HSD17B8	Estradiol 17-beta-dehydrogenase 8
Pa_1_17280	3.3	5.0	Q12428†	PDH1	Probable 2-methylcitrate dehydratase
Pa_1_14630	3.0	6.3	Q8N159	NAGS	N-acetylglutamate synthase
Pa_4_7010	3.0	3.7	Q16698	DECR1	2.4-dienoyl-CoA reductase
Pa_3_10910	3.0	3.3	P15937†	acu-8	Acetyl-CoA hydrolase
Pa_4_8600	3.0	3.0	O15382	BCAT2	Branched-chain-amino-acid aminotransferase
Pa_2_6200	2.3	5.0	P23434	GCSH	Glycine cleavage system H protein
Pa_6_8420	2.3	4.0	P45954	ACADSB	Short/branched chain specific acyl-CoA dehydrogenase
Pa_2_430	2.3	3.3	Q9Y697	NFS1	Cysteine desulfurase‡
Pa_3_2600	2.0	5.3	P40926	MDH2	Malate dehydrogenase
Pa_1_15690	2.0	3.7	Q10341†	cys2	Probable serine-O-acetyltransferase cys2
Pa_2_4980	2.0	3.3	Q16836	HADH	Hydroxyacyl-coenzyme A dehydrogenase
Pa_3_1420	2.0	2.0	Q9UHQ9	CYB5R1	NADH-cytochrome b5 reductase 1
Pa_3_9430	1.7	3.0	P04181	OAT	Ornithine aminotransferase‡
Pa_4_3040	1.7	1.7	P48735	IDH2	Isocitrate dehydrogenase [NADP]
Pa_1_7660	1.7	1.3	Q02252	ALDH6A1	Methylmalonate-semialdehyde dehydrogenase
Pa_7_10210	1.3	3.0	P30084	ECHS1	Enoyl-CoA hydratase
Pa_1_1980	1.3	1.7	P51649	ALDH5A1	Succinate-semialdehyde dehydrogenase‡
Pa_4_660	1.3	1.3	P34897	SHMT2	Serine hydroxymethyltransferase‡
Electron Transport Chain and Respiration
Pa_1_14370	2.7	2.3	O75947	ATP5H	ATP synthase subunit d
Pa_4_7160	2.0	4.7	O75489	NDUFS3	NADH dehydrogenase iron-sulfur protein 3
Pa_1_8620	2.0	1.7	O75306	NDUFS2	NADH dehydrogenase iron-sulfur protein 2§
Pa_5_7500	1.3	1.7	O14561	NDUFAB1	Acyl carrier protein
Pa_6_240	1.3	1.3	P47985	UQCRFS1	Cytochrome b-c1 complex subunit Rieske§
Other Pathways
Pa_2_12010	8.7	10.0	P49411	TUFM	Mitochondrial elongation factor Tu‡
Pa_4_1130	2.3	2.3	nhd	—	—
Pa_5_8240	2.0	2.7	P30044	PRDX5	Peroxiredoxin-5
Pa_6_8740	2.0	2.3	P10599	TXN	Thioredoxin

^*P. anserina IDs correspond to the ‘P. anserina Genome Project’ database release version 6.32 (downloaded from http://podospora.igmors.u-psud.fr/).
^†If no human homologue was determinable, if possible a homologue from a fungal species was selected for reference.
^‡Protein whose prokaryotic homologue was identified as a substrate of E. coli CLPXP^20,21.
^§Fe-S containing/binding protein.
Listed are all proteins that were specifically co-purified with both catalytically active (HsCLPP^WT-TAG) and inactive human CLPP (HsCLPP^TRAP-TAG) over the background control sample and therefore classified as potential CLPP interaction partners. For each protein the P. anserina ID, average number of unique peptides identified by MS analyses across all biological replicates of the respective sample as well as Swiss-Prot ID and gene and protein name of the human homologue (Supplementary Table 1) are listed. Categories (e.g. ‘Metabolism’) were assigned based on annotations from the Swiss-Prot database and the general literature. nhd, no homologue determinable.Proteins enriched >1.5-fold in the ΔPaClpP/HsClpP^TRAP-TAG sample over the ΔPaClpP/HsClpP^WT-TAG sample (HsCLPP^TRAP-TAG-enriched) are in bold.

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Table 1 Proteins co-purifying with HsCLPP^WT-TAG and HsCLPP^TRAP-TAG.

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