KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse monoclonal anti-Chlamydia LPS serum | Provided by Dr. Daniel Rockey (Oregon State University) | EVI-H1 |
| Mouse monoclonal anti-inaC (CT813) | Chen et al., 2006 | N/A |
| Rabbit polyclonal anti-GarD/CTL0390 | This study, Thermo | AB3075, Project 1VC2780 |
| Mouse monoclonal anti-Ubiquitin, FK2 | Cayman Chemical | Cat#14220 |
| Rabbit monoclonal anti-Linear Ubiquitin, 1E3 | Sigma | Cat#MABS199, RRID:AB_2576212 |
| Rabbit monoclonal anti-Linear Ubiquitin, 1E3 | Sigma | Cat#ZRB2114 |
| Rabbit monoclonal anti-K48 ubiquitin, Apu2 | Sigma | Cat#ZRB2150 |
| Rabbit monoclonal anti-K63 ubiquitin, Apu3 | Sigma | Cat#05-1308, RRID:AB_1587580 |
| Rabbit polyclonal anti-HOIP | Abcam | Cat#ab46322, RRID:AB_945269 |
| Mouse monoclonal anti-HOIL-1, clone 2E2 | Sigma | Cat#MABC576, RRID:AB_2737058 |
| Rabbit polyclonal anti-p62 (SQSTM1) | MBL International | Cat#PM045, RRID:AB_1279301 |
| Mouse monoclonal anti-NBR1, 5C3 | Abcam | Cat#ab55474, RRID:AB_2149404 |
| CALCOCO2 MaxPab rabbit polyclonal antibody (D01; anti-NDP52) | Abnova | Cat#H00010241-D01, RRID:AB_10633399 |
| Rabbit polyclonal anti-Optineurin | ProteinTech | Cat#10837-1-AP, RRID:AB_2156665 |
| Rabbit polyclonal anti-TAX1BP1 | Bethyl Laboratories | Cat#A303-791A, RRID:AB_11218189 |
| Mouse monoclonal anti-LAMP1 | DSHB | Cat#H4A3, RRID:AB_2296838 |
| Rabbit polyclonal anti-LC3 | MBL International | Cat#PM036, RRID:AB_2274121 |
| Rabbit monoclonal anti-GABARAP+GABARAPL1+GABARAPL2 | Abcam | Cat#ab109364, RRID:AB_10861928 |
| Rabbit polyclonal anti-RNF213 | Sigma | Cat#HPA003347, RRID:AB_1079204 |
| Rabbit polyclonal anti-GAPDH | Abcam | Cat#ab9485, RRID:AB_307275 |
| Rabbit polyclonal anti-SLC1 (CT043) | Saka et al., 2011 | N/A |
| Rabbit polyclonal anti-ISG15 | ProteinTech | Cat#15981-1-AP, RRID:AB_2126302 |
| Goat anti-rabbit AlexaFluor 488 | Invitrogen | Cat#A11034, RRID:AB_2576217 |
| Goat anti-mouse AlexaFluor 488 | Invitrogen | Cat#A11029, RRID:AB_138404 |
| Donkey anti-rabbit AlexaFluor 568 | Invitrogen | Cat#A10042, RRID:AB_2534017 |
| Goat anti-mouse AlexaFluor 568 | Invitrogen | Cat#A11004, RRID:AB_2534072 |
| Goat anti-rabbit AlexaFluor 660 | Invitrogen | Cat#A21073, RRID:AB_10374435 |
| Goat anti-mouse AlexaFluor 660 | Invitrogen | Cat#A21054, RRID:AB_1500635 |
| Goat anti-rabbit IgG, HRP | Invitrogen | Cat#65-6120, RRID:AB_2533967 |
| Goat anti-mouse IgG, HRP | Invitrogen | Cat#62-6520, RRID:AB_2533947 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Recombinant human interferon gamma (IFN-γ) | Millipore | Cat#IF005 |
| Critical Commercial Assays | ||
| SYTOX™ Green Nucleic Acid Stain | Invitrogen | Cat#S7020 |
| Deposited Data | ||
| Raw sequencing data for whole genomes of C. trachomatis mutant library hits (Sequence Read Archive) | This study | SRA: PRJNA865907 |
| Original western blot and emicroscopy images (Mendeley Data) | This study | ; doi: 10.17632/hkvx8gx2ft.1 |
| H2P2 database and web portal | L. Wang et al., 2018 | http://h2p2.oit.duke.edu/H2P2Home/ |
| ESBL database of Human E3 Ubiquitin Ligases | Medvar et al., 2016 | https://esbl.nhlbi.nih.gov/Databases/KSBP2/Targets/Lists/E3-ligases/ |
| Experimental Models: Cell Lines | ||
| Vero cells | ATCC | CCL-81, RRID:CVCL_0059 |
| A549 cells | ATCC | CCL-185, RRID:CVCL_0023 |
| HFF-1 cells | ATCC | SCRC-1041, RRID:CVCL_3285 |
| Primary cervical epithelial cells (HCerEpiC) | ScienCell | Cat#7060, lot #16983 |
| HOIP KO A549s, clone #1 | This study | N/A |
| HOIP KO A549s, clone #2 | This study | N/A |
| HOIL-1 KO A549s, clone #1 | This study | N/A |
| HOIL-1 KO A549s, clone #2 | This study | N/A |
| RNF213 KO A549s, pool #1 | This study | N/A |
| RNF213 KO A549s, pool #2 | This study | N/A |
| RNF213 KO A549s, pool #3 | This study | N/A |
| ISG15 knockout A549s | Bhushan et al., 2020 | N/A |
| Experimental Models: Organisms/Strains | ||
| Chlamydia trachomatis, serovar LGV-L2/434/Bu | Haldar et al., 2016 | N/A |
| Chlamydia trachomatis, serovar LGV-L2/434/Bu + pGFP::SW2 | Haldar et al.; 2016, Wang et al., 2011 | N/A |
| Chlamydia muridarum MoPn + pGFP::CM | Haldar et al., 2016; Liu et al., 2014 | N/A |
| Chlamydia trachomatis, serovar LGV-L2/434/Bu RifR | Kokes et al., 2015; Nguyen & Valdivia, 2012 | N/A |
| Chlamydia trachomatis, serovar LGV-L2/434/Bu chemical mutant library (CTL2M library) | Kokes et al., 2015 | N/A |
| Chlamydia trachomatis, serovar LGV-L2/434/Bu incA− (CTL2M0923, CTL0374 R197*) + p2TK2-SW2-incDprom-mCherry-incDterm | Kokes et al., 2015; Sixt et al., 2017 | N/A |
| Chlamydia trachomatis, serovar LGV-L2/434/Bu + p2TK2-SW2-incDprom-mCherry-incDterm | Sixt et al., 2017 | N/A |
| Chlamydia trachomatis, serovar D/UW-3/Cx (CtD) | Yang et al., 2021 | N/A |
| Chlamydia trachomatis, serovar D/UW-3/Cx CT135R201* (CtD CT135−) | Yang et al., 2021 | N/A |
| Chlamydia trachomatis, serovar LGV-L2/434/Bu CTL0390::bla (garD::GII strain #1) | This study | N/A |
| Chlamydia trachomatis, serovar LGV-L2/434/Bu CTL0390::bla (garD::GII strain #2) | This study | N/A |
| Chlamydia trachomatis, serovar LGV-L2/434/Bu CTL0390::bla (garD::GII strain #3) | This study | N/A |
| Chlamydia trachomatis, serovar LGV-L2/434/Bu CTL0390::bla +pGFP::SW2 (garD::GII+ pGFP::SW2) | This study | N/A |
| Chlamydia trachomatis, serovar LGV-L2/434/Bu + pBOMB4-MCI | Bauler et al. 2014; This study | N/A |
| Chlamydia trachomatis, serovar LGV-L2/434/Bu + pGarD | This study | N/A |
| Chlamydia trachomatis, serovar LGV-L2/434/Bu garD::GII +pBOMB4-MCI | This study | N/A |
| Chlamydia trachomatis, serovar LGV-L2/434/Bu garD::GII +pGarD | This study | N/A |
| Oligonucleotides | ||
| *see Supplementary Table S1 for primer information* | ||
| Recombinant DNA | ||
| pGFP::SW2 | Wang et al., 2011 | N/A |
| pDFTT3aadA | Lowden et al., 2015 | N/A |
| pDFTT3aadA-CTL0390-1 (pKO-390-1) | This study | N/A |
| pDFTT3aadA-CTL0390-2 (pKO-390-2) | This study | N/A |
| pBOMB4-MCI | Bauler et al., 2014 | GenBank accession no. KF790907 |
| pDFTT3aadA-CTL0390-3 (pKO-390-3) | This study | N/A |
| pBOMB4-ctl0390prom-CTL0390-ctl0390term (pGarD) | This study | N/A |
| pSpCas9(BB)-2A-Puro (PX459) V2.0 | Ran et al., 2013 | RRID:Addgene_62988 |
| Software and Algorithms | ||
| Prism 9.4 | GraphPad Software, LLC | https://www.graphpad.com/scientific-software/prism/ |
| ImageJ 1.53k | NIH | https://imagej.nih.gov/ij/ |
| Fiji 2.3.0 | ImageJ | https://fiji.sc/ |
| Geneious Prime 1.0 | Biomatters Ltd., Dotmatics | https://www.geneious.com/prime/ |
| Alphafold v2.1.0 | Jumper et al., 2021 | (https://colab.research.google.com/github/deepmind/alphafold/blob/main/notebooks/AlphaFold.ipynb |
| PLINK v1.9 | Chang et al., 2015; Purcell et al., 2007 | https://www.cog-genomics.org/plink/ |
| Other | ||
| SNAP2 web tool | Hecht et al., 2015 | https://www.rostlab.org/services/snap/ |
| BioRender | BioRender.com | https://biorender.com/ |
| R script to make Quantile-Quantile plot and statistics in Figure 5A | This study | See Methods S1 or (https://github.com/lw157/PopulationGenetics/blob/master/fast_qqplot.R) |