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Image Lab Biorad Graphpad Prism 9 Graphpad Software Maxquant V 1 6 17 0 Tyanova Et, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 99/100, based on 36433 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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other:Article Title: Microprotein SMIM26 drives oxidative metabolism via serine-responsive mitochondrial translation. Article Snippet: Article Microprotein SMIM26 drives oxidative metabolism via serine-responsive mitochondrial translation Graphical abstract Highlights • CRISPR screen identifies SMIM26 as linking the folate cycle to complex I biogenesis • SMIM26-SFXN1/2-mitoribosome triad promotes serinedependent mt-ND5 translation • SMIM26 loss disrupts mitochondrial tRNA modifications and impairs complex I assembly • SMIM26 is essential for embryonic development and tumor growth in folate-dependent AML Authors Jiemin Nah, Sreya Mahendran, Baptiste Kerouanton, ..., Gregory S. Ducker, David A. Stroud, Lena Ho Correspondence lena@ho-lab.org In brief Nah et al. identify the microprotein SMIM26 as a critical link between mitochondrial serine metabolism and complex I biogenesis.. By scaffolding serine transporters and mitoribosomes, SMIM26 enables nutrient-responsive translation of mt-ND5, revealing a metabolite-gated mechanism for respiratory complex assembly with implications for development and cancer metabolism.. Nah et al., 2025, Molecular Cell 85, 1–17 July 17, 2025 © 2025 Elsevier Inc. All rights are reserved, including those for text and data mining, AI training, and similar technologies. https://doi.org/10.1016/j.molcel.2025.05.033 ll Molecular Cell 85, 1, July 17, 2025 © 2025 Elsevier Inc. 1 All rights are reserved, including those for text and data mining, AI training, and similar technologies. Article Title: Unbiased proteomic profiling of host cell extracellular vesicle composition and dynamics upon HIV-1 infection. Article Snippet: Reagents and Tools table (continued) Reagent/Resource Reference or Source Identifier or Catalog Number Methyl-cellulose, viscosity:25cP Sigma Cat#M6385 Protein A-gold CMC, UMC Utrecht, Netherlands L-arginine-13C6 Thermo Scientific Cat#88210 L-lysine-4,4,5,5-D4 Thermo Scientific Cat#88437 L-arginine-13C6 15N4 Thermo Scientific Cat#89990 L-lysine-13C6 15N2 Thermo Scientific Cat#88209 Dialyzed Fetal Bovine Serum Thermo Scientific Cat#A3382001 SDS Roth CN30.3 Tris-HCl pH 8.0 Sigma #T6666 Acetone Fischer Chemical #A/0600/17 Acetonitrile Merck Cat#1.00029.1000 Urea Sigma Cat#U5378 Dithiothreitol (DTT) Euromedex Cat#EU0006-B Idodoacetamide Sigma Cat#I6125 LysC Wako #129-02541 Trypsin Promega Cat#V5111 Trifluoroacetic acid (TFA), Sigma Cat#73645 SDB-RPS solid phase extraction material VWR #66886-U 50-cm column with 75-μm inner diameter, packed in-house with 1.8- μm C18 particles Dr. Maisch GmbH C18 column (75 lm inner diameter × 2 cm; nanoViper Acclaim PepMapTM 100, Thermo Scientific Cat#164535 50 cm × 75 lm C18 column (nanoViper Acclaim PepMapTM RSLC, 2 lm, 100 A,) Thermo Scientific Cat#164942 Article Title: ATG4 family proteins drive phagophore growth independently of the LC3/GABARAP lipidation system. Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Paraview; Version 5.7.0-RC2 ISBN 978-1930934306 RRID:SCR_002516 Blender; Versions 2.79 (For X3D import) & 2.80 (Rendering) Blender Foundation RRID:SCR_008606 Prism; Version 7.02 GraphPad RRID: SCR_002798 Image Lab software; Recombinant:Article Title: Dissecting the Roles of Mitochondrial Complex I Intermediate Assembly Complex Factors in the Biogenesis of Complex I. Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-ATP5A (IB: 1/1000) Abcam Cat# ab14748, RRID: AB_301447 Anti-COA1 (IB: 1/500) Sigma-Aldrich Cat# HPA011944, RRID: AB_1848671 Anti-Core 1 (IB: 1/1000) ThermoFisher Cat# 459140, RRID: AB_2532227 Anti-COX1 (IB: 1/1000) ThermoFisher Cat# 459600, RRID: AB_2532240 Anti-COX2 (IB: 1/1000) ThermoFisher Cat# A-6404, RRID: AB_221584 Anti-COX4 (IB: 1/1000) Abcam Cat# ab110261, RRID: AB_10862101 Anti-Cytochrome c (IB: 1/500) BD labs Cat# 556433, RRID: AB_396417 Anti-Flag M2 clone (IB: 1/1000) Sigma-Alrich Cat# F1804, RRID: AB_262044 Anti-Mic10 (IB: 1/1000) Aviva Systems Biology Cat# ARP44801_P050, RRID: AB_2045181 Anti-NDUFA13 (IB: 1/1000) Abcam Cat# ab110240, RRID: AB_10863178 Anti-NDUFB8 (IB: 1/1000) Abcam Cat# ab110242, RRID: AB_10859122 Anti-NDUFC2 (IB: 1/1000) Santa Cruz Cat# sc-398719 Anti-NDUFS2 (IB: 1/1000) Abcam Cat# ab110249, RRID: AB_10861985 Anti-NDUFS3 (IB: 1/1000) Innovative Research Cat# A21343, RRID: AB_1501824 Anti-SDHA (IB: 1/1000) Abcam Cat# ab14715, RRID: AB_301433 Anti-TIM29 (IB: 1/1000) Sigma-Aldrich Cat# HPA041858, RRID: AB_10963429 Anti-TIMMDC1 (IB: 1/500) Sigma-Aldrich Cat# HPA053214, RRID: AB_2682081 Anti-TMEM126B (IB: 1/500) Sigma-Aldrich Cat# HPA014480, RRID: AB_1858083 Anti-TOM20 (IB: 1/1000) Santa Cruz Cat# sc-11415, RRID: AB_2207533 Anti-ACAD9 (IB: 1/500) In house N/A Anti-ECSIT (IB: 1/500) In house N/A Anti-Mfn2 (IB: 1/500) In house N/A Anti-mtHSP70 (IB: 1/500) In house N/A Anti-NDUFA9 (IB: 1/500) In house N/A Anti-NDUFAF1 (IB: 1/500) In house N/A Anti-NDUFB6 (IB: 1/500) In house N/A Anti-NDUFS5 (IB: 1/500) In house N/A Anti-ND1 (IB: 1/500) Gift from A. Lombes (Paris) N/A Anti-TOM40 (IB: 1/500) Gift from M. Mori (Kumamoto) N/A Chemicals, Peptides, and Recombinant Proteins Anisomycin Sigma-Aldrich A9789 EXPRE35S35S Protein Labeling Mix, [35S]-, 7mCi (74MBq), 50mM Tricine (pH 7.4), 10mM 2-mercaptoethanol Perkin Elmer NEG072007MC Puromycin InvivoGen ant-pr-1 Carbonyl cyanide 30- chlorophenylhydrazone Sigma-Aldrich C2759 Anti-Flag M2 Affinity gel Sigma-Aldrich A2220 Flag peptide Sigma-Aldrich F3290 Digitonin- High purity Merck 300410 Dithiobis(succinimidyl propionate) Pierce 22585 Streptavidin magnetic beads ThermoFisher 88816 Biotin Sigma-Aldrich B4639 Chloramphenicol Sigma-Aldrich C0378 (Continued on next page) e1 Cell Reports 31, 107541, April 21, 2020 .. REAGENT or RESOURCE SOURCE IDENTIFIER Proteinase K, from Tritirachium album Sigma-Aldrich P6556 Deposited Data Raw MS data on PRIDE This paper PRIDE: PXD018075 Experimental Models: Cell Lines HEK293T cells ATCC CRL-3216 143B TK- osteosarcoma cells Trounce et al., 1994 N/A 143B TK- r0 osteosarcoma cells Trounce et al., 1994 N/A Flp-In T-REx HEK293 cells ThermoFisher Scientific Cat#: R75007; RRID: CVCL_U427 Flp-In T-REx HEK293 AGKKO cells Kang et al., 2017 N/A Recombinant DNA pBABE-NDUFAF1Flag This paper N/A pBABE-NDUFAF1BirA This paper N/A pBABE-ECSITFlag This paper N/A pBABE-ACAD9Flag This paper N/A pBABE-TMEM126BFlag This paper N/A pBABE-TIMMDC1Flag This paper N/A pBABE-TMEM186 Flag This paper N/A pLVX-COA1Flag This paper N/A pLVX-COA1-GFPFlag This paper N/A pLVX-COA1DIMS-GFPFlag This paper N/A Software and Article Title: Mitochondrial microproteins link metabolic cues to respiratory chain biogenesis. Article Snippet: Ph Eur Merck Cat#1.00063.2500 Chloroform, >99.0%(GC) Kanto Chemical Cat#07278-00 EXPRE35S35S Protein Labeling Mix, [35S]-, 2mCi (74MBq), 50mM Tricine (pH 7.4), 10mM 2-mercaptoethanol Perkin Elmer Cat#NEG072002MC L-Methionine. reagent grade, R98% (HPLC) Sigma-Aldrich Cat#M9625 L-Cysteine, 97% Sigma-Aldrich Cat#168149 Sodium carbonate, BioUltra, anhydrous, R99.5% (calc. on dry substance, T) Sigma-Aldrich Cat#71345 Insulin solution human, sterile-filtered, BioXtra, suitable for cell culture Sigma-Aldrich Cat#I9278 IGF-I human Animal-component free, recombinant, expressed in E. coli, R98% (SDS-PAGE), R98% (HPLC), suitable for cell culture Sigma-Aldrich Cat#SRP3069 AICAR MCE Cat#HY-13417 DMEM/High glucose (4500mg/mL) with L-glutamine; without sodium pyruvate HyClone Cat#SH30022.01 DMEM/Low glucose (1000mg/mL) with L-glutamine, sodium pyruvate HyClone Cat#SH30021.01 DMEM, high glucose, no glutamine, no methionine, no cystine Gibco Cat#21013024 Sodium pyruvate solution, 100 mM, sterile-filtered, BioReagent, suitable for cell culture Sigma-Aldrich Cat#S8636 Penicillin-Streptomycin (10,000 U/mL) Gibco Cat#15140-122 Fetal Bovine Serum, South American Origin, Heat Inactivated HyClone Cat#SV30160.03 Fetal Bovine Serum, dialyzed, US origin Gibco Cat#26400-044 TritonTM X-100, laboratory grade Sigma-Aldrich Cat#X100 (Continued on next page) Cell Reports 40, 111204, August 16, 2022 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Cell lines Human HEK293T ATCC Cat#CRL-3216 Mouse C2C12 ATCC Cat#CRL-1772 Experimental models: Organisms/strains Mouse: WT (C57BL/6J) The Jackson Laboratory Cat#000664 Mouse: BR / (C57BL/6J) This paper NA Oligonucleotides For genotyping primers, gRNAs, and qPCR primers, see Table S3 N/A N/A Recombinant DNA lentiCRISPRv2 puro Gift from Shang Li Lab NA psAAV-CMV-mBrawnin-FLAG This paper NA psAAV-CMV-mSmim4-FLAG This paper NA psAAV-CMV-GFP This paper NA pCDH-CMV-mSmim4-FLAG This paper NA pCDH-CMV-mBrawnin-FLAG This paper NA pCDH-CMV-mC16orf91-FLAG This paper NA pCDH-CMV-mUqcc1-FLAG This paper NA pCDH-CMV-mUqcc3-FLAG This paper NA pCDH-CMV-mUqcrq-FLAG This paper NA Software and algorithms ImageJ Schneider et al., 2012 https://imagej.nih.gov/ij/ Image Lab Software for Software:Article Title: Dissecting the Roles of Mitochondrial Complex I Intermediate Assembly Complex Factors in the Biogenesis of Complex I. Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-ATP5A (IB: 1/1000) Abcam Cat# ab14748, RRID: AB_301447 Anti-COA1 (IB: 1/500) Sigma-Aldrich Cat# HPA011944, RRID: AB_1848671 Anti-Core 1 (IB: 1/1000) ThermoFisher Cat# 459140, RRID: AB_2532227 Anti-COX1 (IB: 1/1000) ThermoFisher Cat# 459600, RRID: AB_2532240 Anti-COX2 (IB: 1/1000) ThermoFisher Cat# A-6404, RRID: AB_221584 Anti-COX4 (IB: 1/1000) Abcam Cat# ab110261, RRID: AB_10862101 Anti-Cytochrome c (IB: 1/500) BD labs Cat# 556433, RRID: AB_396417 Anti-Flag M2 clone (IB: 1/1000) Sigma-Alrich Cat# F1804, RRID: AB_262044 Anti-Mic10 (IB: 1/1000) Aviva Systems Biology Cat# ARP44801_P050, RRID: AB_2045181 Anti-NDUFA13 (IB: 1/1000) Abcam Cat# ab110240, RRID: AB_10863178 Anti-NDUFB8 (IB: 1/1000) Abcam Cat# ab110242, RRID: AB_10859122 Anti-NDUFC2 (IB: 1/1000) Santa Cruz Cat# sc-398719 Anti-NDUFS2 (IB: 1/1000) Abcam Cat# ab110249, RRID: AB_10861985 Anti-NDUFS3 (IB: 1/1000) Innovative Research Cat# A21343, RRID: AB_1501824 Anti-SDHA (IB: 1/1000) Abcam Cat# ab14715, RRID: AB_301433 Anti-TIM29 (IB: 1/1000) Sigma-Aldrich Cat# HPA041858, RRID: AB_10963429 Anti-TIMMDC1 (IB: 1/500) Sigma-Aldrich Cat# HPA053214, RRID: AB_2682081 Anti-TMEM126B (IB: 1/500) Sigma-Aldrich Cat# HPA014480, RRID: AB_1858083 Anti-TOM20 (IB: 1/1000) Santa Cruz Cat# sc-11415, RRID: AB_2207533 Anti-ACAD9 (IB: 1/500) In house N/A Anti-ECSIT (IB: 1/500) In house N/A Anti-Mfn2 (IB: 1/500) In house N/A Anti-mtHSP70 (IB: 1/500) In house N/A Anti-NDUFA9 (IB: 1/500) In house N/A Anti-NDUFAF1 (IB: 1/500) In house N/A Anti-NDUFB6 (IB: 1/500) In house N/A Anti-NDUFS5 (IB: 1/500) In house N/A Anti-ND1 (IB: 1/500) Gift from A. Lombes (Paris) N/A Anti-TOM40 (IB: 1/500) Gift from M. Mori (Kumamoto) N/A Chemicals, Peptides, and Recombinant Proteins Anisomycin Sigma-Aldrich A9789 EXPRE35S35S Protein Labeling Mix, [35S]-, 7mCi (74MBq), 50mM Tricine (pH 7.4), 10mM 2-mercaptoethanol Perkin Elmer NEG072007MC Puromycin InvivoGen ant-pr-1 Carbonyl cyanide 30- chlorophenylhydrazone Sigma-Aldrich C2759 Anti-Flag M2 Affinity gel Sigma-Aldrich A2220 Flag peptide Sigma-Aldrich F3290 Digitonin- High purity Merck 300410 Dithiobis(succinimidyl propionate) Pierce 22585 Streptavidin magnetic beads ThermoFisher 88816 Biotin Sigma-Aldrich B4639 Chloramphenicol Sigma-Aldrich C0378 (Continued on next page) e1 Cell Reports 31, 107541, April 21, 2020 .. REAGENT or RESOURCE SOURCE IDENTIFIER Proteinase K, from Tritirachium album Sigma-Aldrich P6556 Deposited Data Raw MS data on PRIDE This paper PRIDE: PXD018075 Experimental Models: Cell Lines HEK293T cells ATCC CRL-3216 143B TK- osteosarcoma cells Trounce et al., 1994 N/A 143B TK- r0 osteosarcoma cells Trounce et al., 1994 N/A Flp-In T-REx HEK293 cells ThermoFisher Scientific Cat#: R75007; RRID: CVCL_U427 Flp-In T-REx HEK293 AGKKO cells Kang et al., 2017 N/A Recombinant DNA pBABE-NDUFAF1Flag This paper N/A pBABE-NDUFAF1BirA This paper N/A pBABE-ECSITFlag This paper N/A pBABE-ACAD9Flag This paper N/A pBABE-TMEM126BFlag This paper N/A pBABE-TIMMDC1Flag This paper N/A pBABE-TMEM186 Flag This paper N/A pLVX-COA1Flag This paper N/A pLVX-COA1-GFPFlag This paper N/A pLVX-COA1DIMS-GFPFlag This paper N/A Software and Article Title: Targeted protein degradation in Escherichia coli using CLIPPERs. Article Snippet: Reagents and tools table Reagent/resource Reference or source Identifier or catalogue number Experimental models E. coli Top10 Laboratory strain collection F– mcrA DE(mrr-hsdRMSmcrBC) φ80lacZ DE(M15) DE(lacX)74 recA1 araD139 DE(ara-leu)7697 galU galK λ– rpsL(StrR) endA1 nupG E. coli BL21 (DE3) Laboratory strain collection F– ompT hsdSB (rB–, mB–) gal dcm (DE3) E. coli C43 (DE3) Laboratory strain collection F– ompT hsdSB (rB–, mB–) gal dcm (DE3) lacUV5p E. coli BW25113 Keio collection (Baba et al, 2006) F– rrnB DElacZ4787 HsdR514 DE(araBAD)567 DE(rhaBAD) 568 rph-1 E. coli J42W07 Keio collection (Baba et al, 2006) BW25113 DE(clpP)::kan E. coli JW0428 Keio collection (Baba et al, 2006) BW25113 DE(clpX)::kan E. coli JW0866 Keio collection (Baba et al, 2006) BW25113 DE(sspB)::kan Recombinant DNA pBAD-6xHis-SUMOClpX Klimecka et al, 2021 pET28a-6xHis-SUMOClpP Klimecka et al, 2021 pET28a-6xHis-SUMOSspB Klimecka et al, 2021 pET28a-His-ZBD This study Reagent/resource Reference or source Identifier or catalogue number pET28a-GroEL This study pET28a-6xHis-SUMOXB-GGS This study pET28a-6xHis-SUMOGGS-SBP This study pET28a-6xHis-SUMOXB-GGS-SBP This study pBAD-His-TEV-cAbGFP This study pBAD-6xHIS-TEV Klimecka et al, 2021 pBAD-6xHis-TEV-eGFP Addgene Cat #54762 pBAD-6xHis-TEV-eGFPssrA Klimecka et al, 2021 pBAD-6xHis-TEV-eGFPAANDENY Klimecka et al, 2021 pBAD-6xHis-TEV-eGFP2xAANDENY Klimecka et al, 2021 pBAD-6xHis-TEV-eGFPXB This study pBAD-6xHis-TEV-eGFPsXB This study pBAD-6xHis-TEV-eGFPIGF This study pBAD-6xHis-TEV-eGFPIGL This study pBAD-myc This study pBAD-myc-XB-GGS This study pBAD-myc-GGS-SBP This study pBAD-myc-XB-GGS-SBP This study pBAD-myc-XBGGSGGSGG-SBP This study pBAD-myc-NRLLLTG This study pBAD-myc-XB-GGSNRLLLTG This study pBAD-myc-XB-GGSGGNRLLLTG This study pBAD-myc-pyrrhocoricin This study pBAD-myc-XB-GGSpyrrhocoricin This study pBAD-myc-XBGGSGGSGGpyrrhocoricin This study Chemicals, enzymes and other reagents Antibodies Mouse anti-GroEL Invitrogen MA3-022 Rabbit anti-enolase Gift from Professor Ben Luisi Goat anti-rabbit Alexa Fluor 488 Invitrogen A11008 Goat anti-mouse Alexa Fluor 647 Invitrogen A32728 10 EMBO reports © The Author(s) D ow nloaded from https://w w w .em bopress.org on June 27, 2025 from IP 2402:800:6390:65e4:88d:215d:4430:6344. .. Reagent/resource Reference or source Identifier or catalogue number Oligonucleotides PCR primers Thermo Fisher Scientific; this study Appendix Table S3 Oligonucleotides Thermo Fisher Scientific; this study Appendix Table S3 Peptides GroTAC3 KareBay Biochem; this study Appendix Table S4 Synthetic GroTAC1, GroTAC2, Anchor-Linker, Linker-Bait GeneScript; this study Appendix Table S4 Software Article Title: Nucleosomal asymmetry shapes histone mark binding and promotes poising at bivalent domains. Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER CBX7 ChIP-seq data Morey et al.43 GEO: GSE42466 TAF3 ChIP-seq data Liu et al.42 GEO: GSE30959 KAT6A/B KO RNA-seq data This paper GEO: GSE250570 Raw Western blot, gel, and microscopy imaging data This paper Mendeley Data: https://doi.org/ 10.17632/5h3565w2p7.1 Experimental models: Cell lines ES-E14TG2a E14 mouse ESCs ATCC Cat# CRL-1821; RRID:CVCL_9108 HA-KAT6B (homozygous tag knockin), derived from ES-E14TG2a This paper N/A HA-KATB; MLL2 Y2688A (homozygous knockin), derived from ES-E14TG2a This paper N/A HA-KATB; EZH1/2 dKO (EZH2-/-; EZH1-/-), derived from ES-E14TG2a This paper N/A HA-KATB; ING5 Y188A (homozygous knockin), derived from ES-E14TG2a This paper N/A HA-KATB; KAT6B D290A (homozygous knockin), derived from ES-E14TG2a This paper N/A HA-KATB; BRPF1 D270/272A (homozygous knockin), derived from ES-E14TG2a This paper N/A HA-KATB; BRPF2 D212/214A (homozygous knockin), derived from ES-E14TG2a This paper N/A KAT6A-/- KO, derived from ES-E14TG2a This paper N/A KAT6B-/- KO, derived from ES-E14TG2a This paper N/A KAT6A-/- KO; KAT6B-/- KO, derived from ES-E14TG2a This paper N/A Oligonucleotides Primers for RT-qPCR, see Table S5 This paper N/A Primers for ChIP-qPCR, see Table S5 This paper N/A Recombinant DNA pX458 Addgene Cat# 48138; RRID:Addgene_48138 pET-3a Novagen Cat# 69418 pET-3d Novagen Cat# 69421 Histone H4 (X. laevis, in pET-3a) Luger et al.87 N/A Histone H3 (X. laevis, in pET-3d) Luger et al.87 N/A Histone H2A (human, in pET-3a) This paper N/A Histone H2B (human, in pET-3a) This paper N/A Histone H3D1–31T32C C110A (in pET-3a) This paper N/A Histone H3D1–44T45C C110A (in pET-3a) This paper N/A Histone H3-His (in pET-3a) Voigt et al.21 N/A Histone H3-Strep (in pET-3a) Voigt et al.21 N/A Histone H3D1–31T32C C110A - His (in pET-3a) This paper N/A Histone H3D1–44T45C C110A – Strep (in pET-3a) This paper N/A Histone H3D1–44T45C C110A – Strep (in pET-3a) This paper N/A Histone H3X (in pET-3a) This paper N/A Histone H3Y (in pET-3a) This paper N/A Histone H3XD1–31T32C C110A (in pET-3a) This paper N/A Histone H3YD1–44T45C C110A (in pET-3a) This paper N/A TAF3 PHD-eGFP-6x His (in pET-28) Villaseñor et al.88 N/A CBX7 chromo-eGFP-6x His (in pET-28) Villaseñor et al.88 N/A (Continued on next page) Molecular Cell 85, 1–19.e1–e12, February 6, 2025 e4 .. REAGENT or RESOURCE SOURCE IDENTIFIER Murine KAT6B MYST domain, aa 426–682, with N-terminal His tag (in pET-3a) This paper N/A Software and algorithms MaxQuant v1.6.1.0 Cox and Article Title: Mitochondrial microproteins link metabolic cues to respiratory chain biogenesis. Article Snippet: Ph Eur Merck Cat#1.00063.2500 Chloroform, >99.0%(GC) Kanto Chemical Cat#07278-00 EXPRE35S35S Protein Labeling Mix, [35S]-, 2mCi (74MBq), 50mM Tricine (pH 7.4), 10mM 2-mercaptoethanol Perkin Elmer Cat#NEG072002MC L-Methionine. reagent grade, R98% (HPLC) Sigma-Aldrich Cat#M9625 L-Cysteine, 97% Sigma-Aldrich Cat#168149 Sodium carbonate, BioUltra, anhydrous, R99.5% (calc. on dry substance, T) Sigma-Aldrich Cat#71345 Insulin solution human, sterile-filtered, BioXtra, suitable for cell culture Sigma-Aldrich Cat#I9278 IGF-I human Animal-component free, recombinant, expressed in E. coli, R98% (SDS-PAGE), R98% (HPLC), suitable for cell culture Sigma-Aldrich Cat#SRP3069 AICAR MCE Cat#HY-13417 DMEM/High glucose (4500mg/mL) with L-glutamine; without sodium pyruvate HyClone Cat#SH30022.01 DMEM/Low glucose (1000mg/mL) with L-glutamine, sodium pyruvate HyClone Cat#SH30021.01 DMEM, high glucose, no glutamine, no methionine, no cystine Gibco Cat#21013024 Sodium pyruvate solution, 100 mM, sterile-filtered, BioReagent, suitable for cell culture Sigma-Aldrich Cat#S8636 Penicillin-Streptomycin (10,000 U/mL) Gibco Cat#15140-122 Fetal Bovine Serum, South American Origin, Heat Inactivated HyClone Cat#SV30160.03 Fetal Bovine Serum, dialyzed, US origin Gibco Cat#26400-044 TritonTM X-100, laboratory grade Sigma-Aldrich Cat#X100 (Continued on next page) Cell Reports 40, 111204, August 16, 2022 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Cell lines Human HEK293T ATCC Cat#CRL-3216 Mouse C2C12 ATCC Cat#CRL-1772 Experimental models: Organisms/strains Mouse: WT (C57BL/6J) The Jackson Laboratory Cat#000664 Mouse: BR / (C57BL/6J) This paper NA Oligonucleotides For genotyping primers, gRNAs, and qPCR primers, see Table S3 N/A N/A Recombinant DNA lentiCRISPRv2 puro Gift from Shang Li Lab NA psAAV-CMV-mBrawnin-FLAG This paper NA psAAV-CMV-mSmim4-FLAG This paper NA psAAV-CMV-GFP This paper NA pCDH-CMV-mSmim4-FLAG This paper NA pCDH-CMV-mBrawnin-FLAG This paper NA pCDH-CMV-mC16orf91-FLAG This paper NA pCDH-CMV-mUqcc1-FLAG This paper NA pCDH-CMV-mUqcc3-FLAG This paper NA pCDH-CMV-mUqcrq-FLAG This paper NA Software and algorithms ImageJ Schneider et al., 2012 https://imagej.nih.gov/ij/ Image Lab Software for Polymerase Chain Reaction:Article Title: Targeted protein degradation in Escherichia coli using CLIPPERs. Article Snippet: Reagents and tools table Reagent/resource Reference or source Identifier or catalogue number Experimental models E. coli Top10 Laboratory strain collection F– mcrA DE(mrr-hsdRMSmcrBC) φ80lacZ DE(M15) DE(lacX)74 recA1 araD139 DE(ara-leu)7697 galU galK λ– rpsL(StrR) endA1 nupG E. coli BL21 (DE3) Laboratory strain collection F– ompT hsdSB (rB–, mB–) gal dcm (DE3) E. coli C43 (DE3) Laboratory strain collection F– ompT hsdSB (rB–, mB–) gal dcm (DE3) lacUV5p E. coli BW25113 Keio collection (Baba et al, 2006) F– rrnB DElacZ4787 HsdR514 DE(araBAD)567 DE(rhaBAD) 568 rph-1 E. coli J42W07 Keio collection (Baba et al, 2006) BW25113 DE(clpP)::kan E. coli JW0428 Keio collection (Baba et al, 2006) BW25113 DE(clpX)::kan E. coli JW0866 Keio collection (Baba et al, 2006) BW25113 DE(sspB)::kan Recombinant DNA pBAD-6xHis-SUMOClpX Klimecka et al, 2021 pET28a-6xHis-SUMOClpP Klimecka et al, 2021 pET28a-6xHis-SUMOSspB Klimecka et al, 2021 pET28a-His-ZBD This study Reagent/resource Reference or source Identifier or catalogue number pET28a-GroEL This study pET28a-6xHis-SUMOXB-GGS This study pET28a-6xHis-SUMOGGS-SBP This study pET28a-6xHis-SUMOXB-GGS-SBP This study pBAD-His-TEV-cAbGFP This study pBAD-6xHIS-TEV Klimecka et al, 2021 pBAD-6xHis-TEV-eGFP Addgene Cat #54762 pBAD-6xHis-TEV-eGFPssrA Klimecka et al, 2021 pBAD-6xHis-TEV-eGFPAANDENY Klimecka et al, 2021 pBAD-6xHis-TEV-eGFP2xAANDENY Klimecka et al, 2021 pBAD-6xHis-TEV-eGFPXB This study pBAD-6xHis-TEV-eGFPsXB This study pBAD-6xHis-TEV-eGFPIGF This study pBAD-6xHis-TEV-eGFPIGL This study pBAD-myc This study pBAD-myc-XB-GGS This study pBAD-myc-GGS-SBP This study pBAD-myc-XB-GGS-SBP This study pBAD-myc-XBGGSGGSGG-SBP This study pBAD-myc-NRLLLTG This study pBAD-myc-XB-GGSNRLLLTG This study pBAD-myc-XB-GGSGGNRLLLTG This study pBAD-myc-pyrrhocoricin This study pBAD-myc-XB-GGSpyrrhocoricin This study pBAD-myc-XBGGSGGSGGpyrrhocoricin This study Chemicals, enzymes and other reagents Antibodies Mouse anti-GroEL Invitrogen MA3-022 Rabbit anti-enolase Gift from Professor Ben Luisi Goat anti-rabbit Alexa Fluor 488 Invitrogen A11008 Goat anti-mouse Alexa Fluor 647 Invitrogen A32728 10 EMBO reports © The Author(s) D ow nloaded from https://w w w .em bopress.org on June 27, 2025 from IP 2402:800:6390:65e4:88d:215d:4430:6344. .. Reagent/resource Reference or source Identifier or catalogue number Oligonucleotides PCR primers Thermo Fisher Scientific; this study Appendix Table S3 Oligonucleotides Thermo Fisher Scientific; this study Appendix Table S3 Peptides GroTAC3 KareBay Biochem; this study Appendix Table S4 Synthetic GroTAC1, GroTAC2, Anchor-Linker, Linker-Bait GeneScript; this study Appendix Table S4 Software Real-time Polymerase Chain Reaction:Article Title: Mitochondrial microproteins link metabolic cues to respiratory chain biogenesis. Article Snippet: Ph Eur Merck Cat#1.00063.2500 Chloroform, >99.0%(GC) Kanto Chemical Cat#07278-00 EXPRE35S35S Protein Labeling Mix, [35S]-, 2mCi (74MBq), 50mM Tricine (pH 7.4), 10mM 2-mercaptoethanol Perkin Elmer Cat#NEG072002MC L-Methionine. reagent grade, R98% (HPLC) Sigma-Aldrich Cat#M9625 L-Cysteine, 97% Sigma-Aldrich Cat#168149 Sodium carbonate, BioUltra, anhydrous, R99.5% (calc. on dry substance, T) Sigma-Aldrich Cat#71345 Insulin solution human, sterile-filtered, BioXtra, suitable for cell culture Sigma-Aldrich Cat#I9278 IGF-I human Animal-component free, recombinant, expressed in E. coli, R98% (SDS-PAGE), R98% (HPLC), suitable for cell culture Sigma-Aldrich Cat#SRP3069 AICAR MCE Cat#HY-13417 DMEM/High glucose (4500mg/mL) with L-glutamine; without sodium pyruvate HyClone Cat#SH30022.01 DMEM/Low glucose (1000mg/mL) with L-glutamine, sodium pyruvate HyClone Cat#SH30021.01 DMEM, high glucose, no glutamine, no methionine, no cystine Gibco Cat#21013024 Sodium pyruvate solution, 100 mM, sterile-filtered, BioReagent, suitable for cell culture Sigma-Aldrich Cat#S8636 Penicillin-Streptomycin (10,000 U/mL) Gibco Cat#15140-122 Fetal Bovine Serum, South American Origin, Heat Inactivated HyClone Cat#SV30160.03 Fetal Bovine Serum, dialyzed, US origin Gibco Cat#26400-044 TritonTM X-100, laboratory grade Sigma-Aldrich Cat#X100 (Continued on next page) Cell Reports 40, 111204, August 16, 2022 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Cell lines Human HEK293T ATCC Cat#CRL-3216 Mouse C2C12 ATCC Cat#CRL-1772 Experimental models: Organisms/strains Mouse: WT (C57BL/6J) The Jackson Laboratory Cat#000664 Mouse: BR / (C57BL/6J) This paper NA Oligonucleotides For genotyping primers, gRNAs, and qPCR primers, see Table S3 N/A N/A Recombinant DNA lentiCRISPRv2 puro Gift from Shang Li Lab NA psAAV-CMV-mBrawnin-FLAG This paper NA psAAV-CMV-mSmim4-FLAG This paper NA psAAV-CMV-GFP This paper NA pCDH-CMV-mSmim4-FLAG This paper NA pCDH-CMV-mBrawnin-FLAG This paper NA pCDH-CMV-mC16orf91-FLAG This paper NA pCDH-CMV-mUqcc1-FLAG This paper NA pCDH-CMV-mUqcc3-FLAG This paper NA pCDH-CMV-mUqcrq-FLAG This paper NA Software and algorithms ImageJ Schneider et al., 2012 https://imagej.nih.gov/ij/ Image Lab Software for |