KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| anti-AGK, mouse monoclonal | AB Clonal Technology; This study | clone 506-1-1-1 |
| anti-ALAS1 (clone EPR10247), rabbit monoclonal | Abcam | Cat#ab154860 |
| anti-ANT1, mouse monoclonal | Lu et al., 2017 | clone IF3F11 |
| anti-ANT2, rabbit polyclonal | Pacific Immunology; This study | clone 5695 |
| anti-ANT2/3 (clone 5H7), mouse monoclonal | Panneels et al., 2003 | N/A |
| anti-ATP5B, rabbit polyclonal | Peter Pedersen, JHU | N/A |
| anti-β-actin, mouse monoclonal | Sigma-Aldrich | Cat#A5441; RRID:AB_476744 |
| anti-COX4, rabbit polyclonal | Abcam | Cat#16056; RRID:AB_443304 |
| anti-CPOX, rabbit polyclonal | Proteintech | Cat# 12211-1-AP; RRID:AB_2084233 |
| anti-CYTB, rabbit polyclonal | Proteintech | Cat#55090-1-AP; RRID:AB_2881266 |
| anti-CYTC (clone 7H8.2C12), mouse monoclonal | BD Biosciences | Cat# 556433; RRID:AB_396417 |
| anti-DNAJC19, rabbit polyclonal | Proteintech | Cat#12096-1-AP; RRID:AB_2094914 |
| anti-FECH, rabbit polyclonal | Proteintech | Cat#14466-1-AP; RRID:AB_2231579 |
| anti-GRP75, mouse monoclonal | Antibodies Inc. | Cat#75-127 |
| anti-HA (clone HA-7), mouse monoclonal | Sigma-Aldrich | Cat#H9658; RRID:AB_439705 |
| anti-MTCO1 (clone 1D6E1A8), mouse monoclonal | Thermo Fisher Scientific | Cat#459600; RRID:AB_2532240 |
| anti-MTCO2 (clone 12C4F12), mouse monoclonal | Thermo Fisher Scientific | Cat#A-6404; RRID:AB_221584 |
| anti-NDUFB6 (clone 21C11BC11), mouse monoclonal | Abcam | Cat#ab110244; RRID:AB_10865349 |
| anti-NDUFS1 (clone EPR11521(B)), rabbit monoclonal | Abcam | Cat#ab169540; RRID:AB_2687932 |
| anti-NDUFV1, rabbit polyclonal | Proteintech | Cat#11238-1-AP; RRID:AB_2149040 |
| anti-NDUFV2, rabbit polyclonal | Proteintech | Cat#15301-1-AP; RRID: AB_2149048 |
| anti-OPA1 (clone 18), mouse monoclonal | BD Biosciences | Cat#612606; RRID:AB_399888 |
| anti-Protein C (clone HPC4), rabbit polyclonal | Genscript | Cat#A01774-100; RRID:AB_2744686 |
| anti-PHB1 (clone 6031), rabbit polyclonal | BioLegend | Cat#603102; RRID:AB_2164630 |
| anti-PHB2 (clone 6118), rabbit polyclonal | BioLegend | Cat#611802; RRID:AB_2164497 |
| anti-SDHA (clone 2E3GC12FB2AE2), mouse monoclonal | Invitrogen/Abcam | Cat#459200; RRID:AB_2532231/Cat# ab14715; RRID:AB_301433 |
| anti-SDHB (clone 21A11AE7), mouse monoclonal | Abcam | Cat#ab14714; RRID:AB_301432 |
| anti-SFXN1, rabbit polyclonal | Proteintech | Cat#12296-1-AP; RRID:AB_2185814 |
| anti-SFXN2, rabbit polyclonal | Sigma-Aldrich | Cat#HPA026834; RRID:AB_1856791 |
| anti-SFXN3, rabbit polyclonal | Sigma-Aldrich | Cat#HPA048105; RRID:AB_2680265 |
| anti-SFXN4, rabbit polyclonal | Cusabio | Cat#CSB-PA744046LA01HU |
| anti-SFXN5, rabbit polyclonal | Cusabio | Cat#CSB- PA819464LA01HU |
| anti-TIMM22 (clone EPR9973), rabbit monoclonal | Abcam | Cat#ab167423; RRID:AB_2802138 |
| anti-TIMM23, mouse monoclonal | BD Biosciences | Cat#611332; RRID:AB_398755 |
| anti-TIMM50, rabbit polyclonal | Proteintech | Cat#22229-1-AP; RRID:AB_2879039 |
| anti-TOMM20, rabbit polyclonal | Santa Cruz Biotechnology | Cat# sc-11415 (discontinued); Cat# sc-17764; RRID:AB_2207533 |
| anti-UQCRC2 (clone 13G12), mouse monoclonal | Abcam | Cat# ab14745; RRID:AB_2213640 |
| anti-UQCRFS1 (clone 5A5), mouse monoclonal | Abcam | Cat#ab14746; RRID:AB_301445 |
| Goat anti-rabbit IgG (H+L), secondary antibody, HRP | Thermo Fisher Scientific | Cat#31460; RRID:AB_228341 |
| Goat anti-mouse IgG (H+L), secondary antibody, HRP | Thermo Fisher Scientific | Cat#62-6520; RRID:AB_2533947 |
| Chemicals, peptides, and recombinant proteins | ||
| anisomycin | Sigma-Aldrich | Cat#A9789 |
| blasticidin | InvivoGen | Cat#ant-bl-05 |
| 1,4-benzoquinone | Sigma-Aldrich | Cat#PHR1028 |
| BPTES | Tocris | Cat#5301 |
| coenzyme Q9 | Sigma-Aldrich | Cat#27597 |
| coenzyme Q10 | Sigma-Aldrich | Cat#C9538 |
| cytochrome c | Sigma-Aldrich | Cat#C2506 |
| decylubiquinone | Enzo Life Science | Cat#BML-CM115 |
| dialyzed FBS | Gemini Bio; Thermo Fisher Scientific | Cat#100-108; Cat#A3382001 |
| digitonin | Biosynth International | Cat#D-3200 |
| n-dodecyl-β-maltoside | Thermo Fisher Scientific | Cat#D4641 |
| 4,6-Dioxoheptanoic acid (succinylacetone) | Sigma-Aldrich | Cat#D1415 |
| DMEM, with 4.5 g/L glucose and L-glutamine, without sodium pyruvate | Corning | Cat#10-013-CM |
| DMEM, with 4.5 g/L glucose, L-glutamine, and sodium pyruvate | GIBCO | Cat#11995040 |
| DMEM without glucose | GIBCO | Cat#11966025 |
| DMEM with L-glutamine, without D-glucose, without L-arginine HCl, without L-lysine HCl, without sodium pyruvate | GIBCO | Cat#ME120220 |
| DMEM with high glucose, no glutamine, no methionine, no cystine | GIBCO | Cat#21013024 |
| DMEM without glucose, glutamine, serine, glycine, and sodium pyruvate | US Biological | Cat#D9800-16 |
| EasyTag™ EXPRESS35S protein labeling mix | Perkin Elmer | Cat#NEG772002MC |
| Fetal Bovine Serum | Seradigm; GIBCO | Cat#1500; Cat#16000-044 |
| Fugene HD Transfection Reagent | Promega | Cat#E2311 |
| deferoxamine mesylate salt | Sigma-Aldrich | Cat#D9533 |
| dimethyl α-ketoglutarate | Sigma-Aldrich | Cat#349631 |
| D(+)-galactose | Acros Organics | Cat#150615000 |
| D(+)-glucose | RPI | Cat#G32040 |
| etomoxir | Tocris | Cat#4539 |
| glycine | RPI | Cat#G36050 |
| hemin | Sigma-Aldrich | Cat#51280 |
| hygromycin B | Thermo Fisher Scientific | Cat#10687010 |
| L-alanine | RPI | Cat#A20060 |
| L-arginine:HCl | Acros Organics | Cat#AC105000250 |
| L-cystine dihydrochloride | RPI | Cat#C81060 |
| L-glutamine | GIBCO | Cat#25030081 |
| 1X GlutaMAX™ | GIBCO | Cat#35050061 |
| L-lysine:2HCl | Acros Organics | Cat#AC413360250 |
| 2H4-L-Lysine:2HCl | Cambridge Isotope Laboratories | Cat#CLM-2247-H-PK |
| 13C6-L-Arginine:HCl | Cambridge Isotope Laboratories | Cat#CLM-2265-H-PK |
| 13C615N2-L-Lysine:2HCl | Cambridge Isotope Laboratories | Cat#CNLM-291-H-PK |
| 13C615N4-L-Arginine:HCl | Cambridge Isotope Laboratories | Cat#CNLM-539-H-PK |
| L-serine | RPI | Cat#S22020 |
| oxalic acid dihydrate | Sigma-Aldrich | Cat#O0376 |
| palmitoyl-L-carnitine chloride | Sigma-Aldrich | Cat#P1645 |
| potassium borohydride | Sigma-Aldrich | Cat#455571 |
| Platinum™ Pfx DNA polymerase | Thermo Fisher Scientific | Cat#11708 |
| Pronase E | Sigma-Aldrich | Cat#7433-2 |
| penicillin-streptomycin | GIBCO | Cat#15140122 |
| puromycin | GIBCO | Cat#A11138 |
| sn-glycerol 3-phosphate lithium salt | Sigma-Aldrich | Cat#94124 |
| sodium bicarbonate | Acros Organics | Cat#S233 |
| sodium formate | Sigma-Aldrich | Cat#71539 |
| sodium pyruvate | GIBCO | Cat#11360070 |
| [U-13C]D-glucose | Cambridge Isotope Laboratories | Cat#CLM-1396-5 |
| [U-13C]L-glutamine | Cambridge Isotope Laboratories | Cat#CLM-1822-H-PK |
| [U-13C]L-serine | Cambridge Isotope Laboratories | Cat#CLM-1574-H |
| UK-5099 | Tocris | Cat#4186 |
| uridine | Sigma-Aldrich | Cat#U3750 |
| zeocin | Thermo Fisher Scientific | Cat#R25001 |
| Critical commercial assays | ||
| Complex I Enzyme Activity Microplate Assay Kit | Abcam | Cat#ab109721 |
| Complex II Enzyme Activity Microplate Assay Kit | Abcam | Cat#ab109908 |
| Complex IV Human Enzyme Activity Microplate Assay Kit | Abcam | Cat#ab109909 |
| DL-Serine Assay Kit | Biovision | Cat#K743 |
| dodecyltrimethylammonium bromide | Sigma-Aldrich | Cat#D8638 |
| Glycine Assay Kit | Biovision | Cat#K589 |
| GoScript™ Reverse Transcription Mix, Oligo(dT) | Promega | Cat#A2791 |
| PureLink™ RNA Mini Kit | Thermo Fisher Scientific | Cat#12183018A |
| PureLink™ DNase Set | Thermo Fisher Scientific | Cat#12185010 |
| Gentra Puregene Cell Kit | QIAGEN | Cat#158767 |
| T7 endonuclease assay | Genecopoeia | Cat#IC005 |
| Seahorse XF Mito Stress Test Kit | Agilent | Cat#103015-100 |
| Seahorse XF Glycolysis Stress Test Kit | Agilent | Cat#103020-100 |
| Pierce™ BCA Protein Assay Kit | Thermo Fisher Scientific | Cat#23225 |
| Cell Titer Glo 2.0 | Promega | Cat#G9241 |
| ALT Assay Kit | Sigma-Aldrich | Cat#MAK052 |
| GDH Assay Kit | Sigma-Aldrich | Cat#MAK099 |
| EXPRESS One-Step SYBR GreenER Kit | Cat#11780200 | |
| CyQUANT Cell Proliferation Assay | Thermo Fisher Scientific | Cat#C7026 |
| NAD/NADH-Glo™ Assay | Promega | Cat#G9071 |
| NADP/NADPH-Glo™ Assay | Promega | Cat#G9081 |
| Deposited data | ||
| SILAC proteomics (HEK293 WT versus AGK KOs) | This study | PRIDE: PXD019826 |
| Experimental models: cell lines | ||
| Human: Flp-In™ 293 | Thermo Fisher Scientific | Cat#R75007 |
| Human: HeLa | ATCC | Cat#CCL-2 |
| Human: 293 SFXN1 KO | This study | N/A |
| Human: HeLa SFXN1 KO | This study | N/A |
| Human: 293 SFXN1 KO + SFXN1 | This study | N/A |
| Human: 293 SFXN1 KO + CNAP-SFXN1 | This study | N/A |
| Human: 293 SFXN1 KO + SFXN1-HA | This study | N/A |
| Human: 293 AGK KO1 | This study | N/A |
| Human: 293 AGK KO2 | This study | N/A |
| Human: 293 AGK KO + AGK | This study | N/A |
| Human: 293 AGK KO + AGKG126E | This study | N/A |
| Human: control fibroblasts | Reyes et al., 2018 | N/A |
| Human: TIMM50 mut fibroblasts | Reyes et al., 2018 | N/A |
| Recombinant DNA | ||
| pcDNA5/FRT | Thermo Fisher Scientific | Cat#V6010-20 |
| pOG44 | Thermo Fisher Scientific | Cat#V600520 |
| pSpCas9(BB)-2A-Puro (PX459) V2.0 | Addgene | Cat#62988 |
| pEF6-nls-YFP-2A-Cas9 | Bowman et al., 2017 | N/A |
| pET28a | Novagen | Cat#69864 |
| PX459-SFXN1-1 | This study | N/A |
| PX459-SFXN1-2 | This study | N/A |
| pEF6-nls-YFP-2A-Cas9-agk1-1 | This study | N/A |
| pcDNA5/FRT-SFXN1 | This study | N/A |
| pcDNA5/FRT-CNAP-SFXN1 | This study | N/A |
| pcDNA5/FRT-SFXN1-HA | This study | N/A |
| pcDNA5/FRT-AGK | This study | N/A |
| pcDNA5/FRT-AGKG126E | This study | N/A |
| pET28a-AGK | This study | N/A |
| pET28a-hANT2 | This study | N/A |
| Software and algorithms | ||
| Proteome Discoverer Software Suite ver 2.0 | Thermo Scientific | N/A |
| MultiQuant ver 3 | AB SCIEX | N/A |
| Quantity One 1-D Analysis Software | Biorad | N/A |
| Prism 8 | Graphpad | N/A |
| FluoChemQ | Cell Biosciences, Inc. | N/A |