Table 2. Proteins identified as potential CLPXP substrates.

P. anserina ID*	Avg. Number of Unique Peptides†	Swiss-Prot ID	Gene	Protein
Chaperones
Pa_6_5510	7.3	Q8NBU5	ATAD1	ATPase family AAA domain-containing protein 1
Pa_6_5590	3.7	O76031	CLPX	ATP-dependent Clp protease ATP-binding subunit clpX-like§
Metabolism
Pa_6_5560	15.7	Q02218	OGDH	2-oxoglutarate dehydrogenase E1 component
Pa_6_1640	7.7	P31327	CPS1	Carbamoyl-phosphate synthetase I§ (Pa_6_1640 matches to small chain/N-terminal region)
Pa_7_9520	7.3	O00330	PDHX	Pyruvate dehydrogenase protein X component
Pa_5_5370	5.0 (x3.8)	P36957	DLST	2-oxoglutarate dehydrogenase E2 component
Pa_7_10050	4.0	P08559	PDHA1	Pyruvate dehydrogenase E1 component subunit alpha
Pa_1_13750	2.7	P48728	AMT	Aminomethyltransferase
Pa_5_5810	2.3	P09622	DLD	Dihydrolipoyl dehydrogenase§
Pa_1_15800	2.0	P11177	PDHB	Pyruvate dehydrogenase E1 component subunit beta
Pa_1_20100	1,3	P26440	IVD	Isovaleryl-CoA dehydrogenase
Pa_3_9520	1.3	P35914	HMGCL	Hydroxymethylglutaryl-CoA lyase
Electron Transport Chain
Pa_3_4870	21.0	P28331	NDUFS1	NADH dehydrogenase 75 kDa subunit‖
Pa_4_7950	3.7	P49821	NDUFV1	NADH dehydrogenase flavoprotein 1‖
Pa_5_9670	3.3	Q5T2R2	PDSS1	Decaprenyl-diphosphate synthase subunit 1
Other Pathways
Pa_3_11170	10.7 (x4.0)	O59778‡	bio2	Biotin synthase‖
Pa_1_18430	2.7	P22626	HNRNPA2B1	Heterogeneous nuclear ribonucleoproteins A2/B1
Pa_2_10680	2.0	Q86SX6	GLRX5	Glutaredoxin-related protein 5‖
Pa_1_6330	1.7	Q96RP9	GFM1	Mitochondrial elongation factor G§
Pa_5_2590	1.7	G2TRP3‡	ymr31	Mitochondrial 37S ribosomal protein YMR-31

^*P. anserina IDs correspond to the ‘P. anserina Genome Project’ database release version 6.32 (downloaded from http://podospora.igmors.u-psud.fr/).

^†If the protein was also co-purified with HsCLPP^WT-TAG above threshold, its enrichment factor in the ΔPaClpP/HsClpP^TRAP-TAG sample over the ΔPaClpP/HsClpP^WT-TAG sample is provided in parentheses.

^‡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 CLPXP²⁰,²¹.

^‖Fe-S containing/binding protein.

Listed are all proteins that were either exclusively or highly enriched co-purified with the catalytically inactive variant HsCLPP^TRAP-TAG and therefore classified as potential CLPXP substrates. For each protein, the P. anserina ID, average number of unique peptides identified by MS analyses across all biological replicates as well as Swiss-Prot ID, and gene and protein name of the human homologue (Supplementary Table 2) are listed. Categories (e.g. ‘Metabolism’) were assigned based on annotations from the Swiss-Prot database and the general literature.