Cell Culture:
Virus:Article Title: Clp-targeting BacPROTACs impair mycobacterial proteostasis and survival.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains M. smegmatis mc2-155 ATCC ATCC 700084 M. smegmatis mc2 155 DclpC2::gmR This paper N/A M. smegmatis mc2 155 DclpC3::gmR This paper N/A M. smegmatis mc2 155 DDclpC2clpC3::gmR This paper N/A M. smegmatis 607 DSMZ ATCC 607, DSM 43465 M. tuberculosis H37Rv William R. Jacobs Jr., Albert Einstein College of Medicine H37RvMa (Ioerger et al.44) M. tuberculosis H37Rv DclpC2::hygR This paper N/A VphAE159 Jain et al.45 N/A Chemicals, peptides, and recombinant proteins M. smegmatis ClpC1 Morreale et al.26 N/A M. smegmatis ClpC1DWB This paper N/A M. smegmatis ClpC1DWB-F444A This paper N/A M. smegmatis ClpC1 NTD (1–148) Morreale et al.26 N/A M. smegmatis ClpP1 with his-tag Morreale et al.26 N/A M. smegmatis ClpP2 with his-tag Morreale et al.26 N/A M. smegmatis ClpC2 with his-tag This paper N/A M. smegmatis ClpC2CRD with his-tag This paper N/A M. smegmatis ClpC3 with his-tag This paper N/A BRDTBD1-NrdI Morreale et al. 26 N/A a-casein Sigma-Aldrich Cat#C6780-5G b-casein Sigma-Aldrich Cat#C6905-1G Pyruvate kinase Sigma-Aldrich Cat#9136-5KU Lactic dehydrogenase Sigma-Aldrich Cat#1254-5KU NADH Roche 10128023001 Phosphoenolpyruvate Sigma-Aldrich Cat#860077-1G pArg-JQ1 This paper N/A dCym-JQ1 This paper N/A Homo-BacPROTAC6 Junk et al.29 N/A Homo-BacPROTAC6dis Junk et al.29 N/A dCym6 Junk et al.29 N/A dCym6dis Junk et al.29 N/A Homo-BacPROTAC7 Junk et al.29 N/A Homo-BacPROTAC7dis Junk et al. 29 N/A dCym7 Junk et al.29 N/A dCym7dis Junk et al.29 N/A dCym Barbie and Kazmaier28 N/A dCymM Kiefer et al.46 N/A Ecu* (analogue 6) Hawkins et al.19 N/A Ecu** This paper N/A LVAWG peptide This paper N/A TCEP Sigma-Aldrich Cat#C4706-10G Tween80 Sigma-Aldrich Cat# P1754-500ML Tween20 Sigma-Aldrich Cat#P9416-100ML (Continued on next page) Cell 186, 2176–2192.e1–e12, May 11, 2023 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Streptavidin Prospec cOmplete, EDTA-free Protease inhibitor cocktail Roche 05056489001 Trypsin Promega V5280 BXT buffer Iba lifescience Cat#2-1042-025 Trifluoroacetic Acid Fisher Scientific Cat#11378277 Acetonitrile Merck Cat#113212 Formic acid Sigma-Aldrich 27001-1L-M Iodacetamide Sigma-Aldrich Cat#L6125-25G Bedaquiline MedChemExpress HY-14881 Ethambutol Sigma-Aldrich E4630 SDC Sigma-Aldrich Cat#30970-100G Middlebrook 7H9 Broth Base Sigma-Aldrich M0178-500G BD Difco Middlebrook 7H10 Agar Fisher Scientific DF0627-17-4 HBS-P+ buffer 10x Cytiva Cat#BR100671 Critical commercial assays High Sensitivity DNA Kit Agilent Technologies, Inc. Cat#5067-4626 TruePrep DNA Library Prep Kit V2 for Illumina Vazyme Biotech Co. Cat#TD501 EZ-Link NHS-PEG4 Biotinylation Kit Thermo Fisher Scientific Cat#21455 Amine-coupling kit Cytiva Cat#BR100050 Deposited data Msm ClpC2CRD:pArg Crystal Structure This paper and Protein Data Bank (PDB) 8B9O Mtb ClpC1NTD:Ecu** Crystal Structure This paper and Protein Data Bank (PDB) 8B9U Msm IP-MS proteomics Data of ClpC2 interactome This paper and PRoteomics IDentification Database PXD037231 Msm LFQ proteomics Data of dCym/Ecu* treatment (10 mM) This paper and PRoteomics IDentification Database PXD037232 Msm LFQ proteomics Data of dCym treatment (150 mM) This paper and PRoteomics IDentification Database PXD037234 Msm LFQ proteomics Data of BacPROTAC treatment This paper and PRoteomics IDentification Database PXD037235 Msm MS-PRM Data This paper, PanoramaWeb and PRoteomics IDentification Database PXD037198 Mtb IP-MS proteomics Data of dCym derivative targets This paper and PRoteomics IDentification Database PXD037712 Mtb LFQ proteomics Data of BacPROTAC treatment This paper and PRoteomics IDentification Database PXD037730 Oligonucleotides Primers for generation of M. smegmatis genomic mutants, see Table S5 This paper N/A Primers for generation of M. tuberculosis DclpC2, see Table S5 This paper N/A Primers for construction of plasmids for inducible expression in mycobacteria, see Table S5 This paper N/A Recombinant DNA pET-21a (+) plasmid Addgene https://www.addgene.org/ pMyC plasmid Beckham et al.47 RRID:Addgene_42192 p2NIL plasmid Parish and Stoker48 RRID:Addgene_20188 (Continued on next page) ll OPEN ACCESS e2 Cell 186, 2176–2192.e1–e12, May 11, 2023 Article
Recombinant:Article Title: Clp-targeting BacPROTACs impair mycobacterial proteostasis and survival.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains M. smegmatis mc2-155 ATCC ATCC 700084 M. smegmatis mc2 155 DclpC2::gmR This paper N/A M. smegmatis mc2 155 DclpC3::gmR This paper N/A M. smegmatis mc2 155 DDclpC2clpC3::gmR This paper N/A M. smegmatis 607 DSMZ ATCC 607, DSM 43465 M. tuberculosis H37Rv William R. Jacobs Jr., Albert Einstein College of Medicine H37RvMa (Ioerger et al.44) M. tuberculosis H37Rv DclpC2::hygR This paper N/A VphAE159 Jain et al.45 N/A Chemicals, peptides, and recombinant proteins M. smegmatis ClpC1 Morreale et al.26 N/A M. smegmatis ClpC1DWB This paper N/A M. smegmatis ClpC1DWB-F444A This paper N/A M. smegmatis ClpC1 NTD (1–148) Morreale et al.26 N/A M. smegmatis ClpP1 with his-tag Morreale et al.26 N/A M. smegmatis ClpP2 with his-tag Morreale et al.26 N/A M. smegmatis ClpC2 with his-tag This paper N/A M. smegmatis ClpC2CRD with his-tag This paper N/A M. smegmatis ClpC3 with his-tag This paper N/A BRDTBD1-NrdI Morreale et al. 26 N/A a-casein Sigma-Aldrich Cat#C6780-5G b-casein Sigma-Aldrich Cat#C6905-1G Pyruvate kinase Sigma-Aldrich Cat#9136-5KU Lactic dehydrogenase Sigma-Aldrich Cat#1254-5KU NADH Roche 10128023001 Phosphoenolpyruvate Sigma-Aldrich Cat#860077-1G pArg-JQ1 This paper N/A dCym-JQ1 This paper N/A Homo-BacPROTAC6 Junk et al.29 N/A Homo-BacPROTAC6dis Junk et al.29 N/A dCym6 Junk et al.29 N/A dCym6dis Junk et al.29 N/A Homo-BacPROTAC7 Junk et al.29 N/A Homo-BacPROTAC7dis Junk et al. 29 N/A dCym7 Junk et al.29 N/A dCym7dis Junk et al.29 N/A dCym Barbie and Kazmaier28 N/A dCymM Kiefer et al.46 N/A Ecu* (analogue 6) Hawkins et al.19 N/A Ecu** This paper N/A LVAWG peptide This paper N/A TCEP Sigma-Aldrich Cat#C4706-10G Tween80 Sigma-Aldrich Cat# P1754-500ML Tween20 Sigma-Aldrich Cat#P9416-100ML (Continued on next page) Cell 186, 2176–2192.e1–e12, May 11, 2023 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Streptavidin Prospec cOmplete, EDTA-free Protease inhibitor cocktail Roche 05056489001 Trypsin Promega V5280 BXT buffer Iba lifescience Cat#2-1042-025 Trifluoroacetic Acid Fisher Scientific Cat#11378277 Acetonitrile Merck Cat#113212 Formic acid Sigma-Aldrich 27001-1L-M Iodacetamide Sigma-Aldrich Cat#L6125-25G Bedaquiline MedChemExpress HY-14881 Ethambutol Sigma-Aldrich E4630 SDC Sigma-Aldrich Cat#30970-100G Middlebrook 7H9 Broth Base Sigma-Aldrich M0178-500G BD Difco Middlebrook 7H10 Agar Fisher Scientific DF0627-17-4 HBS-P+ buffer 10x Cytiva Cat#BR100671 Critical commercial assays High Sensitivity DNA Kit Agilent Technologies, Inc. Cat#5067-4626 TruePrep DNA Library Prep Kit V2 for Illumina Vazyme Biotech Co. Cat#TD501 EZ-Link NHS-PEG4 Biotinylation Kit Thermo Fisher Scientific Cat#21455 Amine-coupling kit Cytiva Cat#BR100050 Deposited data Msm ClpC2CRD:pArg Crystal Structure This paper and Protein Data Bank (PDB) 8B9O Mtb ClpC1NTD:Ecu** Crystal Structure This paper and Protein Data Bank (PDB) 8B9U Msm IP-MS proteomics Data of ClpC2 interactome This paper and PRoteomics IDentification Database PXD037231 Msm LFQ proteomics Data of dCym/Ecu* treatment (10 mM) This paper and PRoteomics IDentification Database PXD037232 Msm LFQ proteomics Data of dCym treatment (150 mM) This paper and PRoteomics IDentification Database PXD037234 Msm LFQ proteomics Data of BacPROTAC treatment This paper and PRoteomics IDentification Database PXD037235 Msm MS-PRM Data This paper, PanoramaWeb and PRoteomics IDentification Database PXD037198 Mtb IP-MS proteomics Data of dCym derivative targets This paper and PRoteomics IDentification Database PXD037712 Mtb LFQ proteomics Data of BacPROTAC treatment This paper and PRoteomics IDentification Database PXD037730 Oligonucleotides Primers for generation of M. smegmatis genomic mutants, see Table S5 This paper N/A Primers for generation of M. tuberculosis DclpC2, see Table S5 This paper N/A Primers for construction of plasmids for inducible expression in mycobacteria, see Table S5 This paper N/A Recombinant DNA pET-21a (+) plasmid Addgene https://www.addgene.org/ pMyC plasmid Beckham et al.47 RRID:Addgene_42192 p2NIL plasmid Parish and Stoker48 RRID:Addgene_20188 (Continued on next page) ll OPEN ACCESS e2 Cell 186, 2176–2192.e1–e12, May 11, 2023 Article
Bacteria:Article Title: Bioactive Angucyclines/Angucyclinones Discovered from 1965 to 2023.
Article Snippet: .. Cytotoxic Activities Compound No. Producer Model of Bioactivities Reference 2 Streptomyces sp. HB202 B. subtilis DSM 347, B. epidermidis DSM 20660, D. hominis DSM 7083, K. pneumoniae, P. aeruginosa DSM 50071, S. aureus ATCC 12600, S. aureus, S. epidermidis DSM 20044, S. lentus DSM 6672 [17] 3, 4 Streptomyces sp. QD01-2 S. aureus, B. subtilis, Escherichia coli, Candida albicans [18] 5, 6 Streptomyces sp. QD01-2S. gilvotanarens NRRL 11382 S. aureus, B. subtilis, Escherichia coli, Candida albicans S. aureus ATCC 6538P, B. subtilis No. 10707 [18] [31] 7–9 S. fradiae PTZ0025 S. aureus [19] 10 M. rosaria SCSIO N160 S. cellulosae YIM PH20352 Streptomyces sp. XZHG99T Streptomyces sp. IB201691-2A E. coli ATCC 25922, S. aureus ATCC 29213, B. thuringiensis SCSIO BT01, B. subtilis SCSIO BS01 P. cucumerina, Alternaria panax, F. oxysporum, F. solani, M. smegmatis, S. aureus S. carnosus DSMZ 20501, Erwinia persicina DSMZ 19328 S. carnosus DSMZ 20501, M. smegmatis DSMZ 43286 [20] [59,60] [61] [62] 11 M. rosaria SCSIO N160 E. coli ATCC 25922, S. aureus ATCC 29213,B. thuringiensis SCSIO BT01, B. subtilis SCSIO BS01 [20] 12 M. echinospora SCSIO 04089 S. aureus ATCC 29213, B. thuringensis SCSIO BT01,B. subtilis 1064, M. luteus SCSIO ML01, MRSA shhs-A1 [21] 15 M. echinospora SCSIO 04089 M. luteus SCSIO ML01, [21] 17 S. pratensis KCB-132 A variety of bacteria and fungi [22] 18, 19 S. pratensis KCB-132 B. cereus, C. lagenarium [22] 20 S. pratensis KCB-132 S. aureus CMCC 26003 [23] (–)-21 Streptomyces sp. KCB-132 B. cereus CMCC 32210 [24] 23 Streptomyces sp. KCB-132 S. aureus, Enterococcus faecium [25] 24 S. pratensis KCB-132 E. faecium, S. aureus, K. pneumoniae,A. baumannii, P. aeruginosa, E. species [26] Mar. ..
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