Table 1. Proteins co-purifying with HsCLPPWT-TAG and HsCLPPTRAP-TAG.
| P. anserina ID* | Avg. Number of Unique Peptides HsCLPPWT-TAG | Avg. Number of Unique Peptides HsCLPPTRAP-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.
§Fe-S containing/binding protein.
Listed are all proteins that were specifically co-purified with both catalytically active (HsCLPPWT-TAG) and inactive human CLPP (HsCLPPTRAP-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/HsClpPTRAP-TAG sample over the ΔPaClpP/HsClpPWT-TAG sample (HsCLPPTRAP-TAG-enriched) are in bold.