KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-FLAG M2, Mouse, Monoclonal, Unconjugated | Sigma-Aldrich | Cat# F1804; RRID:AB_262044 |
| Anti-alpha-Tubulin, Mouse, Monoclonal, Unconjugated | Sigma-Aldrich | Cat# T5168; RRID:AB_477579 |
| Anti-Actin, Rabbit, Recombinant, Unconjugated | Abcam | Cat# ab179467 RRID:AB_2737344 |
| Anti-phospho-p38 MAPK (Thr180/Tyr182), Rabbit | Cell Signaling Technology | Cat # 9211S; RRID:AB_331641 |
| Anti-total-p38 MAPK, Rabbit | Peterson et al.(39) | N/A |
| Goat Anti-Rabbit IgG, HRP-linked | Cell Signaling Technology | Cat# 7074; RRID:AB_2099233 |
| Goat Anti-Mouse IgG - H&L, Polyclonal, HRP Conjugated | Abcam | Cat# ab6789; RRID:AB_955439 |
| Anti-GFP, Mouse, Monoclonal, Unconjugated (clones 7.1 and 13.1) | Sigma-Aldrich | Cat# 11814460001; RRID:AB_390913 |
| Bacterial and virus strains | ||
| Escherichia coli OP50 | Brenner(77) | WB Cat# WBStrain00041969; RRID:WB-STRAIN:WBStrain00041969 |
| E. coli HT115(DE3) | Fire et al.(78) | WB Cat# WBStrain00041080; RRID:WB-STRAIN:WBStrain00041080 |
| E. coli DH5α | New England BioLabs | Cat# C2987H |
| E. coli BL21(DE3) | New England BioLabs | Cat# C2527H |
| Pseudomonas aeruginosa (UCBPP-PA14) | Rahme et al.(79) | RRID:WB-STRAIN: WBStrain00041978 |
| P. aeruginosa (PAK) | Lee et al.(73) | N/A |
| P. aeruginosa (PAO1) | Lee et al.(73) | N/A |
| P. aeruginosa PA14 ΔphzA1-G1 ΔphzA2-G2 (Δphz) | Dietrich et al.(49) | N/A |
| P. aeruginosa PA14 ΔgacA | Troemel et al.(7) | N/A |
| P. aeruginosa PA14 ΔrhlR | Rahme et al.(79) | N/A |
| P. aeruginosa PA14 ΔlasR | Fred Ausubel | N/A |
| P. aeruginosa PA14 ΔpqsR | Fred Ausubel | N/A |
| P. aeruginosa PA14 transposon mutants | Liberati et al.(80) | N/A |
| P. aeruginosa PAO1 (pqsE overexpression) | This study | N/A |
| P. aeruginosa PA14 (pqsE overexpression) | This study | N/A |
| Chemicals, peptides, and recombinant proteins | ||
| 5-Fluoro-2’-deoxyuridine | Sigma-Aldrich | Cat# CAF0503 |
| (−) Tetramisole hydrochloride | Sigma-Aldrich | Cat# L9756–10G |
| Q5 High-Fidelity DNA Polymerase | New England BioLabs | Cat# R0101 |
| Isopropyl-β-D-thiogalactoside (IPTG) | GoldBio | Cat# I2481C200 |
| Trizol | Thermo Fisher Scientific | Cat# 15596018 |
| Proteinase K | New England BioLabs | Cat# P8107S |
| Ethylenediaminetetraacetic acid (EDTA), 0.5M, pH 8.0 | Thermo Fisher Scientific | Cat# 1860851 |
| HALT Protease Inhibitor Cocktail (100X) | Thermo Fisher Scientific | Cat# 78430 |
| Phenol:chloroform:isoamyl alcohol | Thermo Fisher Scientific | Cat# 15593031 |
| Phenazine-1-carboxylic acid | Ark Pharm | Cat# AK-98673 |
| Phenazine-1-carboxamide | Princeton BioMolecular Research | Cat# PBMR030086 |
| 1-hydroxyphenazine | TCI America | Cat# H0289 |
| Pyocyanin | Cayman Chemicals | Cat# 10009594 |
| Auxin α-napthaleneacetic acid (K-NAA) | PhytoTech Labs | Cat# N610 |
| SpCas9 Nuclease | IDT | Cat# 1081058 |
| A.s. Cas12a (Cpf1) Ultra | IDT | Cat# 10001273 |
| Ulp1 protease | Thermo Fisher Scientific | Cat# SAE0067 |
| Ni-NTA resin | Qiagen | Cat# 30210 |
| Imidazole | Sigma-Aldrich | Cat# I5513 |
| N-acetyl-L-trytophanamide (NATA) | Sigma-Aldrich | Cat# A6501 |
| Methanol for HPLC | Thermo Fisher Scientific | Cat# 61009–0040 |
| 16% Formaldehyde Solution (w/v) | Thermo Fisher Scientific | Cat# 28908 |
| Gentamycin sulfate | Sigma | Cat# G1264 |
| Streptomycin sulfate | Thermo Fisher Scientific | Cat# AC612240500 |
| Critical commercial assays | ||
| iScript gDNA Clear cDNA Synthesis Kit | Bio-Rad | Cat# 172–5034 |
| DC Protein Assay | Bio-Rad | Cat# 5000111 |
| iTaq Universal SYBR Green Supermix | Bio-Rad | Cat# 172–5120 |
| Q5 Site-Directed Mutagenesis Kit | New England BioLabs | Cat# E0552S |
| NEBuilder HiFi DNA Assembly master mix | New England BioLabs | Cat# E2621 |
| Deposited data | ||
| Raw and analyzed mRNA-Seq data | This study | GSE202258 |
| Experimental models: Organisms/Strains | ||
| C. elegans: Strain: N2 (Bristol) | Brenner(77) | WB Cat# WBStrain00000001; RRID:WB-STRAIN:WBStrain00000001 |
| C. elegans: Strain: AU307 agIs44[irg-4p::gfp::unc-54–3’UTR;myo-2p::mCherry] | Pukkila-Worley et al.(41) | N/A |
| C. elegans: Strain: AY101 acIs101 [pDB09.1(irg-5p::gfp); pRF4(rol-6(su1006))] | Bolz et al.(81) | WB Cat# WBStrain00000322; RRID: WB-STRAIN:WBStrain00 000322 |
| C. elegans: Strain: VL491 nhr-86(tm2590) | Arda et al.(50) | WB Cat# WBStrain00040127; RRID: WB-STRAIN:WBStrain00 040127 |
| C. elegans: Strain: RPW137 nhr-86(ums12) | Peterson et al.(39) | N/A |
| C. elegans: Strain: RPW99 nhr-86(tm2590);agIs44 [irg-4p::gfp::unc-54–3’UTR;myo-2p::mCherry] | Peterson et al.(39) | N/A |
| C. elegans: Strain: RPW106 nhr-86(tm2590);acIs101 [pDB09.1(irg-5p::gfp); pRF4(rol-6(su1006))] | Peterson et al.(39) | N/A |
| C. elegans: Strain: RPW165 nhr-86(ums12); agIs44 [irg-4p::gfp::unc-54–3 ‘ UTR;myo-2p::mCherry] | Peterson et al.(39) | N/A |
| C. elegans: Strain: SJ4100 zcIs13 [hsp-6::gfp + lin-15(+)] | Yoneda et al.(82) | WB Cat # WBStrain00034068; RRID:WB-STRAIN:WBStrain00034068 |
| C. elegans: Strain: CA1200 ieSi57 [eft-3p::TIR1::mRuby::un54 3’UTR + Cbr-unc-119(+)] | Zhang et al.(51) | WB Cat # WBStrain00004055; RRID:WB-STRAIN:WBStrain00004055 |
| C. elegans: Strain: OP318 unc-119(ed3); wgIs318 [nhr-12::TY1::EGFP::3xFLAG(92C12)+unc-119(+)] | Gerstein et al.(56) | WB Cat # WBStrain00030124; RRID:WB-STRAIN:WBStrain00030124 |
| C. elegans: Strain: RPW423 umsEx88[cyp-35C1p::gfp::unc-54–3 ‘ UTR; myo-2p::mCherry] | This study | N/A |
| C. elegans: Strain: RPW348 nhr-86(ums64[NHR-86::AID]); ieSi57 [eft-3p::TIR1::mRuby::un54 3’UTR + Cbr-unc-119(+)] | This study | N/A |
| C. elegans: Strain: RPW424 nhr-86(ums65[3xFLAG::NHR-86]); ieSi57 [eft-3p::TIR1::mRuby::un54 3’UTR + Cbr-unc-119(+)] | This study | N/A |
| C. elegans: Strain: RPW427 nhr-86(ums66[3xFLAG::NHR-86::AID]); ieSi57 [eft-3p::TIR1::mRuby::un54 3’UTR + Cbr-unc-119(+)] | This study | N/A |
| C. elegans: Strain: RPW191 nhr-86(ums14[3xFLAG::NHR-86]) | This study | N/A |
| C. elegans: Strain: RPW401 nhr-86(ums14[3xFLAG::NHR-86]); agIs44 [irg-4p::gfp::unc-54–3 VTR;myo-2p::mCherry] | This study | N/A |
| C. elegans: Strain: RPW430 nhr-86(ums67[3xFLAG::NHR-86[F379H]]);agIs44 [irg-4p::gfp::unc-54- 3’ \JTR;myo-2p::mCherry] | This study | N/A |
| C. elegans: Strain: MGH167 sid-1(qt9); aIxIs9 [vha-6p::s/d-1::SL2::GFP] | Melo et al.(19) | N/A |
| Experimental models: Media | ||
| Bacto peptone | Thermo Fisher Scientific | Cat# 211677 |
| BD Bacto agar | BD | Cat# 214030 |
| Oligonucleotides | ||
| See Table S4 | This study | N/A |
| Recombinant DNA | ||
| pHERD30T | Qiu et al.(83) | NovoPro Cat# V005565 |
| pSMT3 | Yunus et al.(84) | N/A |
| pPD95.75 | Addgene plasmid # 1494 | RRID:Addgene_1494 |
| pHER30T::pqsE | This study | N/A |
| pSMT3::nhr-86 ligand binding domain | This study | N/A |
| pSMT3::nhr-86F379H ligand binding domain | This study | N/A |
| pPD95.75::cyp-35C1p::gfp | This study | N/A |
| Software and algorithms | ||
| Fiji/ImageJ | Schindelin et al.(85) | RRID:SCR_002285 |
| OASIS 2 | Han et al.(86) | RRID:SCR_014450 |
| R Console (Version 3.5) | The R Foundation | RRID:SCR_001905 |
| FastQC (Version 0.11.5) | https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ | RRID:SCR_014583 |
| Kallisto (version 0.45.0) | Bray et al.(87) | RRID:SCR_016582 |
| Sleuth (version 0.30.0) | Pimentel et al.(88) | RRID:SCR_002555 |
| GSEA (version 4.1.0) | Subramanian et al.(89) | RRID:SCR_003199 |
| pheatmap (version 1.0.12) | https://cran.r-project.org/web/packages/pheatmap/index.html | RRID:SCR_016418 |
| WormCat 2.0 | Holdorf et al.(90); Higgins et al.(91) | N/A |
| GraphPad Prism 9 | https://www.graphpad.com/scientific-software/prism/ | RRID:SCR_002798 |
| AlphaFold-Multimer | Evans et al.(92) | N/A |
| Schrodinger v.19–4 | https://www.schrodinger.com | RRID:SCR_014879 |
| Other | ||
| 0.22 μm cellulose Spin-X columns | Thermo Fisher Scientific | Cat# 07–200-386 |
| HPLC screw-top vials with fixed inserts | Agilent Technologies | Cat# 5188–6592 |
| Biphenyl HPLC column (4.6 × 150 mm, 2.6 μm) | Kinetex | Cat# 00F-4622-E0 |
| Dynabead Protein G | Invitrogen | Cat# 10004D |