KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse monoclonal anti Actin | MP Biomedicals | SKU: 0869100-CF, Clone C4 |
| Rabbit polyclonal anti beta-tubulin | Abcam | Cat#: Ab6046, RRID:AB_2210370 |
| Rabbit polyclonal anti IpaH9.8 | EpiGentek | Cat#: A55475 |
| Mouse monoclonal anti Cul1 | ThermoFisher | Cat#: 32–2400, 2H4C9, RRID:AB_86218 |
| Mouse monoclonal anti Myc | Cell Signaling | Cat#: 2276S, RRID:AB_331783 |
| Mouse monoclonal anti FLAG M2-Peroxidase | Millipore Sigma | SKU: A8592, RRID:AB_439702 |
| Mouse monoclonal anti FLAG M2 | Millipore Sigma | SKU: F3165, RRID:AB_259529 |
| Rat monoclonal anti GSDMD | Aglietti et al., 2016 | Clone 17G2G9, Genentech |
| Mouse monoclonal anti Rho-1D4 | University of British Colombia | https://ubc.flintbox.com/technologies/0f1ef64b-fa5d-4a58-9003-3e01f6f672a6 |
| Mouse monoclonal anti-Ubiquitin | LifeSensors | SKU: VU-0101, clone VU-1, RRID:AB_2716558 |
| Human monoclonal anti K11-Ubiquitin | Matsumoto et al., 2010 | Genentech |
| Human monoclonal anti K48-Ubiquitin | Newton et al., 2008 | Genentech |
| Human monoclonal anti K63-Ubiquitin | Newton et al., 2008 | Genentech |
| Rabbit monoclonal anti GSDMD | Cell Signaling Technology | Cat#: 97558S, E8G3F, RRID:AB_2864253 |
| Rabbit monoclonal anti GSDMD(Asp275) | Cell Signaling Technology | Cat#: 36425S, E7H9G, RRID:AB_2799099 |
| Mouse monoclonal caspase-4 | Enzo | Cat#: ADI-AAM-114 RRID:AB_10621609 |
| Bacterial and virus strains | ||
| Shigella flexneri M90T wild-type (WT) | John Rohde, Dalhousie University | N/A |
| Shigella flexneri M90T wild-type (WT) GFP | This study | Genentech |
| Shigella flexneri M90T ΔIpaH7.8 (WT) GFP | This study | Genentech |
| Biological samples | ||
| Chemicals, peptides, and recombinant proteins | ||
| Ultra-pure LPS E. coli 0111:B4 | InvivoGen | Cat#: 0111:B4 |
| Egg phosphatidylcholine (Egg PC) | Avanti Polar Lipids | Cat#: 840051 |
| Egg phosphatidylethanolamine (Egg PE) | Avanti Polar Lipids | Cat#: 840021 |
| Egg Liss Rhod phosphatidylethanolamine | Avanti Polar Lipids | Cat#: 810146 |
| Val-boroPro | Millipore Sigma | Cat#: 531465 |
| Doxycycline | Fisher scientific (Clontech) | Cat#: NC042034 |
| 3X FLAG® Peptide | Millipore Sigma | SKU: F4799 |
| 1D4 peptide (TETSQVAPA) | Genscript | Custom peptide |
| MLN-7243 | ChemieTek | Cat#: CT-M7243 |
| MLN-4924 (Pevonedistat) | ChemieTek | Cat#: CT-M4924 |
| Bortezomib | ChemieTek | Cat#: CT-BZ001 |
| Propidium iodide | Millipore Sigma | SKU: P4170 |
| YOYO-1 Iodide | ThermoFisher | Cat#: Y3601 |
| Nuclight Rapid Red Dye | essenbioscience | Cat#: 4717 |
| Congo Red | Millipore Sigma | SKU: C6277 |
| Poly-L-lysine | Millipore Sigma | SKU: P4707 |
| Alt-R CRISPR-Cas9 | IDT | Cat#: 1081060 |
| IpaH7.8 wild-type (recombinant) | This study | Genentech |
| IpaH7.8 C357A (recombinant) | This study | Genentech |
| Human GSDMD (recombinant) | This study | Genentech |
| Mouse GSDMD (recombinant) | This study | Genentech |
| Human E1 | R&D systems | Cat#: E-304–050 |
| Human UBE2D3 | R&D systems | Cat#: E2–627-100 |
| Human Ubiquitin | R&D systems | Cat#: U-100H-10M |
| K11-linked tetra-Ub chains | R&D systems | Cat#: UC-45–025 |
| K48-linked tetra-Ub chains | R&D systems | Cat#: UC-210B-025 |
| K63-linked tetra-Ub chains | R&D systems | Cat#: UC-310B-025 |
| Critical commercial assays | ||
| CytoTox 96® Non-radioactive Cytotoxicity Assay | Promega | Cat#: G1780 |
| Power SYBR™ Green Cells-to-CT™ Kit | ThermoFisher | Cat#: 4402955 |
| Protein labeling kit RED-MALEIMIDE 2nd Generation | NanoTemper | SKU: MO-L014 |
| Deposited data | ||
| Shigella flexneri whole-genome sequencing | This study | SRA: PRJNA697993 |
| Experimental models: cell lines | ||
| Ea.hy926 human endothelial cells | Genentech gCell facility | N/A |
| Ea.hy926 GSDMD−/− CRISPR-KO cells | This study | N/A |
| 293T human embryonic kidney cells | Genentech gCell facility | N/A |
| HeLa human cervical epithelial cells | Genentech gCell facility | N/A |
| Caco-2 human intestinal epithelial cells | Genentech gCell facility | N/A |
| HeLa GSDMD−/− CRISPR-KO cells | This study | N/A |
| ER-Hoxb8-immortalized murine myeloid progenitor cells | Wang et al., 2006 | Genentech |
| Experimental models: organisms/strains | ||
| Nlrc4−/− mice (C57BL6/N) | Mariathasan et al., 2004 | Genentech |
| Gsdmd−/− mice (C57BL6/N) | Kayagaki et al., 2015 | Genentech |
| Nlrc4−/− Gsdmd−/− mice (C57BL6/N) | This study | Genentech |
| Oligonucleotides | ||
| Human GSDMD gRNA | IDT | TTCCACTTCTACGATGCCA |
| GSDMD RT-qPCR forward primer | IDT | GTGTGTCAACCTGTCTATCAAGG |
| GSDMD RT-qPCR reverse primer | IDT | CATGGCATCGTAGAAGTGGAAG |
| ipaH7.8 RT-qPCR forward primer | IDT | CCCTGATCGTGGAGAACAATAA |
| ipaH7.8 RT-qPCR reverse primer | IDT | CACGGACAGGCGATTGTTA |
| GAPDH RT-qPCR forward primer | IDT | GTCTCCTCTGACTTCAACAGCG |
| GAPDH RT-qPCR reverse primer | IDT | ACCACCCTGTTGCTGTAGCCAA |
| Recombinant DNA | ||
| pMIN-ducer (dox-inducible, lentiviral expression) | Genscript, this study | N/A |
| pMIN-ducer Shigella effector library | Genscript, Table S1, this study | N/A |
| pMIN-ducer FLAG-IpaH7.8 | Genscript, this study | N/A |
| pMIN-ducer FLAG-IpaH7.8 C357A | Genscript, this study | N/A |
| pCDNA3.1 (+) zeo (mammalian transient overexpression) | Genscript, this study | N/A |
| pCDNA3.1 (+) zeo FLAG-IpaH7.8 | Genscript, this study | N/A |
| pCDNA3.1 (+) zeo FLAG-IpaH7.8 C357A | Genscript, this study | N/A |
| pCDNA3.1 (+) zeo FLAG-IpaH7.8 LRR | Genscript, this study | N/A |
| pCDNA3.1 (+) zeo FLAG-IpaH7.8 NEL | Genscript, this study | N/A |
| pCDNA3.1 (+) zeo GSDMA-myc (human) | Genscript, this study | N/A |
| pCDNA3.1 (+) zeo GSDMB-myc (human) | Genscript, this study | N/A |
| pCDNA3.1 (+) zeo GSDMC-myc (human) | Genscript, this study | N/A |
| pCDNA3.1 (+) zeo GSDMD-myc (human) | Genscript, this study | N/A |
| pCDNA3.1 (+) zeo GSDMD-myc (mouse) | Genscript, this study | N/A |
| pCDNA3.1 (+) zeo GSDME-myc (human) | Genscript, this study | N/A |
| pCDNA3.1 (+) zeo GSDMF-myc (human) | Genscript, this study | N/A |
| pCDNA3.1 (+) zeo GSDMD-1D4 (human) | Genscript, this study | N/A |
| pCDNA3.1 (+) zeo GSDMD-1D4 (mouse) | Genscript, this study | N/A |
| pCDNA3.1 (+) zeo GSDMD-1D4 (human) | Genscript, this study | N/A |
| pCDNA3.1 (+) zeo GSDMD-3KR-1D4 (human) | Genscript, this study | N/A |
| pCDNA3.1 (+) zeo GSDMD-15KR-1D4 (human) | Genscript, this study | N/A |
| pCDNA3.1 (+) zeo mmPFD-1D4 (chimera) | Genscript, this study | N/A |
| pCDNA3.1 (+) zeo hsPFD-1D4 (chimera) | Genscript, this study | N/A |
| pCDNA3.1 (+) zeo GSDMD-nLuc-1D4 (human) | Genscript, this study | N/A |
| pCDNA3.1 (+) zeo GSDMD-nLuc-1D4 (mouse) | Genscript, this study | N/A |
| pCDNA3.1 (+) zeo GSDMD-nLuc-1D4 (human 5X Ala mutant, aa 11–15) | Genscript, this study | N/A |
| pCDNA3.1 (+) zeo GSDMD-nLuc-1D4 (human 5X Ala mutant, aa 16–20) | Genscript, this study | N/A |
| pCDNA3.1 (+) zeo GSDMD-nLuc-1D4 (human 5X Ala mutant, aa 21–25) | Genscript, this study | N/A |
| pCDNA3.1 (+) zeo hsGSDMD-mmGSDMD-16–21-1D4 (chimera) | Genscript, this study | N/A |
| pCDNA3.1 (+) zeo mmGSDMD-hsGSDMD-16–20-1D4 (chimera) | Genscript, this study | N/A |
| pCMV-Δ8.9 (lentiviral packaging) | Genentech | N/A |
| pCMV-VSVG (lentiviral packaging) | Genentech | N/A |
| pACYC177 (bacterial kanamycin resistance cassette) | Genentech | N/A |
| pKD46 (lambda red recombinase) | Genentech | N/A |
| pBR322-AmpR-dasher GFP | Genentech | N/A |
| Software and algorithms | ||
| Prism 8 | GraphPad software, LLC | https://www.graphpad.com/, RRID:SCR_002798 |
| DESeq2 | Bioconductor | https://bioconductor.org/packages/release/bioc/html/DESeq2.html, RRID:SCR_015687 |
| MSstats 3.16.0 | Choi et al., 2014 | https://github.com/MeenaChoi/UW2019-MSstats/blob/master/uw2019-msstats.Rmd, RRID:SCR_014353 |
| The R-project | The R Foundation | https://www.r-project.org/ |
| Pymol 2.3.2 | Schrodinger LLC. | https://pymol.org, RRID:SCR_000305 |
| Jalview 2.11.1.4 | The Barton Group, University of Dundee, Scotland, UK | http://www.jalview.org/, RRID:SCR_006459 |
| Incucyte®Base Analysis software | Essenbioscience | https://www.essenbioscience.com/en/products/software/incucyte-base-software/ |
| Other | ||