Guanosine triphosphate

Glutamic acid, succinic acid, adenosine-5′-diphosphate sodium salt (ADP), cytochrome c from bovine heart, malic acid, ethylene glycol-bis-(b-aminoethylether)-N,N,N′N′-tetra acetic acid (EGTA), KH₂PO₄, TrisHCl, ethylenediamine tetra-acetic acid (EDTA), amytal, carboxyatractyloside (CAT), guanosine triphosphate (GTP)quercetin, acetonitrile, 2,2-azinobis (ethyl-2,3-dihydrobenzothiazoline-6-sulphonic acid) diammonium salt (ABTS), potassium persulfate, iron(III) chloride hexahydrate (FeCl₃·6H₂O), 2,4,6-tripyridyl-s-triazine (TPTZ), hydrochloric acid, 6-hydroxy-2,5,7,8-tetramethylchroman-2-carboxylic acid (Trolox) were obtained from “Sigma–Aldrich GmbH”, Steinheim, Germany. Sucrose, mannitol, HEPES, KCl, MgCl₂, trifluoroacetic acid, hyperoside, isoquercitrin, rutin were obtained from “Carl Roth Gmbh”, Karlsruhe, Germany.

Adenosine triphosphate (ATP), creatine phosphate, creatine kinase, and guanosine triphosphate (GTP) were purchased from Sigma-Aldrich (St. Louis, MO, USA). Bovine serum albumin (BSA) conjugated with fluorescein, and 10 kDa dextran conjugated with fluorescein were purchased from Invitrogen (Carlsbad, CA, USA), while 10 kDa dextran conjugated with CF568 was purchased from Biotium (Fremont, CA, USA). A 0.22-µm Millex-GV Filter (#SLGV004SL) was purchased from Millipore (Burlington, MA, USA). Hoechst 33,342 solution was purchased from Dojindo (Kumamoto, Japan), CellMask Deep Red was obtained from Thermo Fisher Scientific (Waltham, MA, USA), and propidium iodide (PI) was procured from Molecular Probes (Eugene, OR, USA). miRNA spike-in control (cel-miR-39) from QIAGEN (Hilden, Germany), miRNA mimic conjugated with Cy3 or Cy5 (hsa-miR-34a, MI0000268; hsa-miR-122, MI0000442; hsa-miR-423, MI0001445; cel-miR-39; MI0000010) from Integrated DNA Technologies (Coralville, IA, USA), and scramble miRNA mimic conjugated with fluorescein (SMC-4001) from Bioneer (Daejeon, Republic of Korea). siRNA duplex for TFEB knockdown from Dharmacon (D-009798–03-0005; Lafayette, CO, USA), and scrambled siRNA from Ambion (Austin, TX, USA). Antibodies and primers were purchased as described in Supplementary Table S1 and S2.

Fluorescein (FAM)-labeled DNA aptamer for the recognition of ATP with the following sequence 5′-TCTCTCACCTGGGGGAGTATTGCGGAGGAAGGT-FAM-3′ has been synthesized by the Laboratory of DNA Sequencing and Oligonucleotides Synthesis, Institute of Biochemistry and Biophysics of the Polish Academy of Sciences (IBB PAS, Warsaw, Poland). The purity of this oligonucleotide was tested with HPLC. Oligomycin A, adenosine 5′-triphosphate disodium salt hydrate grade I (ATP), guanosine triphosphate (GTP), cytidine 5′-triphosphate disodium salt (CTP), uridine 5′-triphosphate trisodium salt dehydrate (UTP), trizma hydrochloride (Tris-HCl), hydrogen peroxide solution (H₂O₂), magnesium chloride (MgCl₂), carbonyl cyanide 4-(trifluoromethoxy)phenylhydrazone (FCCP) and sodium chloride (NaCl), 0.25% Trypsin-EDTA solution were obtained from Sigma-Aldrich Chemical Company (St. Louis, MO, USA).
Fetal bovine serum (FBS) was obtained from Gibco (Rockville, MD, USA). Penicillin/streptomycin and Dulbecco’s modified Eagle’s Medium (DMEM) were obtained from the cell culture company PAA (Immuniq, Warsaw, Poland). All chemicals were of analytical grade purity. Aqueous solutions were prepared with freshly deionized water with 18.2 MΩ cm resistivity (Millipore, Poland). All concentrations of added reagents cited in this paper are final concentrations obtained after mixing, unless otherwise noted.