Key Resources Table
| REAGENT OR RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-ADP-ribose (E6F6A) | Cell Signaling Technologies | Cat. # 83732S RRID: AB_2749858 |
| Anti-ethenoadenosine (1G4) | Thermo Fisher | Cat. # Ma1-40268 RRID: AB_1074293 |
| Anti-vinculin (7F9) | Sigma | Cat. # 90227 RRID:AB_2304338 |
| IRDye 680RD Goat anti-rabbit IgG | LICOR | Cat. # 926-68071 RRID: AB_10956166 |
| IRDye 680RD Goat anti-mouse IgG | LICOR | Cat. # 926-68070 RRID: AB_2651128 |
| Goat anti-rabbit alexa fluor 488 | Thermo Fisher | Cat. # A-11008 RRID: AB_143165 |
| Donkey anti-mouse alexa fluor 488 | Thermo Fisher | Cat. # A-21202 RRID: AB_141607 |
| Anti-paxillin (PXC-10) | Thermo Fisher | Cat. # MA1-24952 RRID: AB_795141 |
| Anti-non-muscle myosin IIA antibody | Abcam | Cat. # ab75590 RRID: AB_10674199 |
| Bacterial strains | ||
| E. coli BL21 | This study | N/A |
| E. coli DE3 | This study | N/A |
| B. stercoris ATCC 43183 | Koropatkin et al., 2008 | N/A |
| B. stercoris ATCC 43183 Δbxa | This study | N/A |
| B. stercoris ATCC 43183 Δtdk | This study | N/A |
| Biological samples | ||
| Strains from human stool from non-IBD and IBD subjects | PRISM cohort at MGH | IRB ref # 2004-P-001067 |
| Cell lines | ||
| HT-29 cells | ATCC | Cat. # HTB-38 |
| Caco-2 cells | ATCC | Cat. # HTB-37 |
| U2OS cells | ATCC | Cat. # HTB-96 |
| Chemicals and reagents | ||
| Ethanol | Sigma | Cat. # 459836 |
| Methanol | Sigma | Cat. # 34860 |
| Inosine | Sigma | Cat. # I4125-10G |
| Hemin | Sigma | Cat. # H9039-1G |
| Vitamin K1 | Sigma | Cat. # V3501-5G |
| M9 salts | Teknova | Cat. # M8008 |
| Ampicillin | Sigma | Cat. # A0166 |
| Gentamicin | Sigma | Cat. # G1397 |
| Erythromycin | Sigma | Cat. # E0774 |
| Kanamycin | Sigma | Cat. # 60615-5G |
| Cellobiose | Becton Dickinson | Cat. # 216010 |
| Maltose | Hardy Diagnostics | Cat. # C6220 |
| Fructose | Sigma | Cat. # F0127 |
| Glucose | Sigma | Cat. # 0188-1Kg |
| TRITC-conjugated Phalloidin | Sigma | Cat. # 90228 |
| DAPI | Sigma | Cat. # 90229 |
| Hoechst | Thermo Fisher | Cat. #62249 |
| SiR actin stain | Cytoskeleton | Cat. # CY-SC001 |
| Fetal Bovine Serum | Thermo Fisher | Cat. # 10438026 |
| Clickable NAD | Biolog | Cat. # N 055 |
| NAD | Sigma | Cat. # 10128965001 |
| Nicotinamide 1,N6-ethenoadenine dinucleotide (etheno-NAD) | Sigma | Cat. # N2630-5MG |
| Fluorescein-NAD | Trevigen | Cat. # 4673-500-01 |
| Tris-HCl pH 8.0 | Thermo Fisher | Cat. # 15568025 |
| Imidazole | Sigma | Cat. # I2399-100G |
| Arginine | Sigma | Cat. # A5006-100G |
| DTT | Sigma | Cat. # 10197777001 |
| PMSF | Thermo Fisher | Cat. # 36978 |
| cOmplete mini-protease inhibitor cocktail (tabs) | Sigma | Cat. # 11836153001 |
| EDTA | Thermo Fisher | Cat. # 15-575-020 |
| Sodium chloride | Sigma | Cat. # S9888 |
| Sucrose | Sigma | Cat. # S0389 |
| Glycerol | Thermo Fisher | Cat. # 15514011 |
| Nitrocellulose membrane | Thermo Fisher | Cat. # IB301002 |
| PVDF membrane | Thermo Fisher | Cat. # IB401031 |
| 15-well 4-20% SDS-PAGE gels | Bio-Rad | Cat. # 4561095 |
| SYBR green | Thermo Fisher | Cat. # A25742 |
| Instant Blue gel stain | Abcam | Cat. # ab119211 |
| His-Pur Nickel beads | Thermo Fisher | Cat. # 88221 |
| Protein G Dynabeads | Thermo Fisher | Cat. # 1004D |
| Tween 20 | Sigma | Cat. # P9416 |
| Triton-X | Sigma | Cat. # X100 |
| Paraformaldehyde | Thermo Fisher | Cat. # 28906 |
| PBS | VWR | Cat. # 45000-446 |
| Blebbistatin | Sigma | Cat. # B0560-1MG |
| ML-9 | Sigma | Cat. # C1172-5MG |
| Crystal Violet | BD Biosciences | Cat. # 212525 |
| Commercial assay kits | ||
| Qiagen RNeasy Plus Mini Kit | Qiagen | Cat. # 74136 |
| Qiagen DNA extraction stool kit | Qiagen | Cat. # 51504 |
| Qiagen Tissue extraction kit | Qiagen | Cat. # 69504 |
| Legendplex Mouse Inflammation Kit | Biolegend | Cat. # 552364 |
| SuperScript III reverse transcriptase kit | Invitrogen | Cat. # 18080051 |
| Direct-Zol RNA MiniPrep Plus | Zymo Research | Cat. # R2060 |
| Fluorometric Inosine Detection Kit | Abcam | Cat. # ab126286 |
| ATP detection kit | Abcam | Cat. # ab113849 |
| ADA activity assay kit | Abcam | Cat. # ab204695 |
| Focal adhesion staining kit | Sigma | Cat. # FAK100 |
| HiFi DNA Assembly Master Mix | New England Biolabs | Cat. # E2621S |
| Q5 High Fidelity DNA Polymerase | New England Biolabs | Cat. # M0491S |
| Deposited Data | ||
| Metabolomic analysis | This study | www.metabolomicsworkbench.org Project ID PR001176 |
| RNA-sequencing data | This study | Sequence Read Archive (SRA), Project ID PRJNA742399 |
| Experimental models | ||
| C57BL/6N mice (Gnotobiotic) | Taconic | B6-M/F |
| C57BL/6N mice (ASF) | Taconic | B6-M/F |
| Plasmids | ||
| pET28b-bxa-snap | This study | N/A |
| pET28b-bxa-818-dbl-cat | This study | N/A |
| pET28b-bxa-719-cat | This study | N/A |
| pET28b-bxa-820-cat | This study | N/A |
| pET28b-bxa | This study | N/A |
| pKNOCK-bla-ermGb | Laurie Comstock; Alexeyev, 1999 |
N/A |
| pKNOCK_erm_BACSTE_02189 | This study | N/A |
| pKNOCK_erm_tdk | This study | N/A |
| Oligonucleotides (5’-3’) | ||
| BS_ADPRT_2_F AGCCCTATGGAGGTGGCTAA |
This study | N/A |
| BS_ADPRT_2_R CTGCCACGTTGGGTACTTCT |
This study | N/A |
| BS_ARH_F GTAGGGCATACCCCAATCCG |
This study | N/A |
| BS_ARH_R TCCTTTAACTCCCTCCGGGT |
This study | N/A |
| BS_SECD_F TGGGACAGGCATCCATCAAC |
This study | N/A |
| BS_SECD_R CCGAGCGACAGTACCATACC |
This study | N/A |
| Bs_tdk_LF_XbaI CCGTCTAGACGCTGAATAATAAGTCAACGGAGTCCG |
This study | N/A |
| Bs_tdk_RF_BamHI GGCGGATCCCGTGTCGCATCTCCGGC |
This study | N/A |
| Bs_bxa_XhoI_F TCCCTCGAGGCGCATCCAACCGCTCC |
This study | N/A |
| Bs_bxa_SalI_R TTAGTCGACGTCGAATGTAATCTTTTTACGTTCCATAGAATCCTGTATTAAATTTATTA |
This study | N/A |
| DEFA_F TGTAGAAAAGGAGGCTGCAATAG |
This study | N/A |
| DEFA_R AGAACAAAAGTCGTCCTGAGC |
This study | N/A |
| REG3G_F ATGCTTCCCCGTATAACCATCA |
This study | N/A |
| REG3G_R GGCCATATCTGCATCATACCAG |
This study | N/A |
| IL22_F TGCTCAACTTCACCCTGG |
This study | N/A |
| IL22_R CTTCTGGATGTTCTGGTCGT |
This study | N/A |
| GAPDH_F AGGTCGGTGTGAACGGATTTG |
This study | N/A |
| GAPDH_R GGGGTCGTTGATGGCAACA |
This study | N/A |
| Software and algorithms | ||
| Prism 9 | GraphPad Software | www.graphpad.com/ |
| FlowJo v11 | FlowJo LLC | www.flowjo.com |
| Tracefinder | Thermo Fisher | www.thermofisher.com/order/catalog/product/OPTON-30491 |
| Progenesis QI | Nonlinear Dynamics | www.nonlinear.com/progenesis/qi/ |
| edgeR | Robinson et al., 2010 | PMID: 19910308 |
| CellQuest | Becton Dickinson | www.bdbiosciences.com |
| PHASTER | Arndt et al., 2016 | www.phaster.ca |
| Harmony High-Content Imaging and Analysis Software v4.9 | Perkin Elmer | www.perkinelmer.com/product/harmony-4-9-office-license-hh17000010 |
| Rich Media and Cell Culture | ||
| 1% vitamin K1-hemin solution | Becton Dickinson | Cat. # 212354 |
| Brain Heart Infusion | Becton Dickinson | Cat. # 241830 |
| Luria Bertani (LB) | Sigma | Cat. # L3522 |
| RPMI 1640 | Thermo Fisher | Cat. # 11875093 |
| DMEM | Thermo Fisher | Cat. # 11965-084 |
| GlutaMAX | Thermo Fisher | Cat. # 35050061 |
| TrypLE-express | Thermo Fisher | Cat. # 12605036 |
| Penicillin-Streptomycin | Thermo Fisher | Cat. # 15140122 |
| Minimal Media | ||
| Menadione | Sigma | Cat. # M5625-100G |
| FeSO4 | Sigma | Cat. # 215422-250G |
| MgCl2 | Sigma | Cat. # M8266-100G |
| CaCl2 | Sigma | Cat. # C5670-100G |
| Hematin | Sigma | Cat. #H3281-5G |
| Vitamin B12 | Sigma | Cat. # V2876-100mg |
| KH2PO4 | Sigma | Cat. # P0662-500G |
| NaCl | Sigma | Cat. # S9888-500G |
| (NH4)2SO4 | Sigma | Cat. # A4915-500G |
| L-cysteine | Sigma | Cat. # C7352-100G |
| Inosine | Sigma | Cat. # I4125-10G |
| Lactose | Sigma | Cat. # I7814-1KG |
| Trace vitamins | ATCC | Cat. # MD-VS |
| Trace minerals | ATCC | Cat. # MD-TMS |