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4 protocols using sirt5

1

SIRT5 Regulation of LDHB Acetylation

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HEK293T, HCT116 and DLD1 cells were purchased from ATCC and cultured in Dulbecco's modified Eagle's medium (DMEM) (Gibco, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (FBS; Gibco). Inhibitors: GW5074 (Selleck Chemicals, Houston, TX, USA), leupeptin (Sigma‐Aldrich, Burlington, MA, USA) and oxamate (Sigma‐Aldrich). Antibodies: SIRT5 (catalogue #15122‐1‐AP, Proteintech, Rosemont, IL, USA), Flag M2 (catalogue #F1804, Sigma‐Aldrich), HA (catalogue #H9658, Sigma‐Aldrich), Ki67 (catalogue #ab16667, Abcam, Cambridge, MA, USA), and cleaved caspase‐3 (catalogue #9661, Cell Signaling Technology, Boston, MA, USA), optineurin (catalogue #ab23666, Abcam), β‐tubulin (catalogue #66240‐1‐Ig, Proteintech), anti‐pan‐acetyl‐lysine (catalogue #9681, Cell Signaling Technology), anti‐pan‐succinylation (catalogue #PTM‐401, PTM Biolabs, Hangzhou, China), anti‐pan‐glutarylation (catalogue #PTM‐1151, PTM Biolabs), anti‐pan‐malonylation (catalogue #PTM‐901, PTM Biolabs), LDHB (catalogue #ab85319, Abcam) and LC3 (catalogue #CY5992, Abways, Shanghai, China). Antibody specifically recognizing acetylation at lysine‐329 of LDHB was prepared commercially at Shanghai HuiOu Biotechnology Co. Ltd (Shanghai, China). Synthesized peptide TLWDIQK(Ac)DLKDL was coupled to KLH as antigen to immunize rabbit. Anti‐serum was collected after five doses of immunization.
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2

Total Protein Extraction and Western Blot

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Total protein was isolated using RIPA lysis buffer (Servicebio, China). The protein with the corresponding volume of loading buffer was boiled in a water bath for 10 min, after which the isolated proteins were separated through SDS-PAGE, transferred to a PVDF membrane, and incubated with primary and secondary antibodies including SIRT1 (Abclonal, A17307), SIRT5 (Proteintech, 15122-1-AP), and actin (Abclonal, AC038).
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3

Protein Modification Detection Protocol

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Anti-acetyllysine (PTM-105), anti-malonyllysine (PTM-901), anti-succinyllysine (PTM-401), anti-glutaryllysine (PTM-1151), anti-succinyllysine conjugated agarose beads (PTM-402), and anti-malonyllysine conjugated agarose beads (PTM-904) were purchased from PTM Biolabs. SIRT5 (Cat# 15122-1-AP, RRID:AB_2188778), NDUFS4 (15849-1-AP), COXIV(Cat# 11242-1-AP, RRID:AB_2085278), and GAPDH (Cat# 60004-1-Ig, RRID:AB_2107436) antibodies were purchased from ProteinTech. ATP5A (Cat# ab14748, RRID:AB_301447), UQCRC2 (Cat# ab14745, RRID:AB_2213640), SDHB (Cat# ab14714, RRID:AB_301432) and COXII (Cat# ab110258, RRID:AB_10887758) were from Abcam. TOM20 (Cat# 612278, RRID:AB_399595) was from BD Biosciences. pCPT-cAMP (C3912-10MG), glucose detection kit (GAGO20-1KT), lactate detection kit (MAK064-1KT), β-hydroxybutyrate assay kit (MAK041) and free fatty acid quantitation kit (MAK044) were from SigmaAldrich. Neutral lipid probe LipidTOX (H34475) was from Invitrogen. Sequencing-grade trypsin (V5113) was purchased from Promega. A list of other chemicals used for lipid chromatography – tandem mass spectrometry (LC-MS/MS) can be found in a previous paper [23 (link)].
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4

Immunoblotting Methodology for Protein Analysis

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Protein preparation and immunoblotting methods were described in previous studies5 (link). The following antibodies were used: aggrecan (Millipore Sigma, AB1031, 1:1000), MMP13 (Abcam, ab39012, 1:1000), SIRT5 (Proteintech, 15122-1-AP, 1:500), TOM20 (Proteintech, 11802-1-AP, 1:1000), AIFM1 (Santa Cruz Biotechnology, sc-13116, 1:500), CHCHD4 (Proteintech, 21090-1-AP, 1:500), NDUFB8 (Complex I) (Abcam, ab192878, 1:2000), SDHB (Complex II) (Abcam, ab175225, 1:2000), UQCRC2 (Complex III) (Absin, abs116449, 1:2000), COX IV (Complex IV) (Cell Signaling Technology, 4844s, 1:2000), ATP5F1A (Complex V) (Abcam, ab176569, 1:2000), and succinylated lysine (PTM Bio, PTM-419, 1:500).
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