KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| anti-FMNL1 (produced in rabbit) | LS Bio | Cat. Nr. LS-C401690; RRID:AB_11210956 |
| anti-ANXA1 (produced in rabbit) | proteintech | Cat. Nr. 21990–1-AP; RRID:AB_11182596 |
| anti-MAP1S (produced in mouse) | Precision antibodies | Cat. Nr. AG10006 |
| anti-TCP1 (produced in rat) | Thermo Fisher | Cat. Nr. MA3–026; RRID:AB_2303275 |
| anti-LASP1 (produced in rabbit) | proteintech | Cat. Nr. 10515–1-AP; RRID:AB_2280966 |
| anti-PHB1 (produced in rabbit) | Cell Signalling | Cat. Nr. #2426; RRID:AB_823689 |
| anti-SACM1L (produced in rabbit) | proteintech | Cat. Nr. 13033–1-AP; RRID:AB_2301284 |
| anti-BCLAF1 (produced in rabbit) | Millipore | Cat. Nr. AB10546; RRID:AB_10806089 |
| anti-VPS39 (produced in rabbit) | proteintech | Cat. Nr. 16219–1-AP; RRID:AB_11043179 |
| anti-GroEL (produced in rabbit) | kind donation from Bukau lab | N/A |
| anti-NPC1 (produced in rabbit) | Thermo Fisher | Cat. Nr. PA1–16817; RRID:AB_2298492 |
| anti-FMNL2 (produced in mouse) | abcam | Cat. Nr. ab57963; RRID:AB_941625 |
| anti-Histone H3 (D1H2) (produced in rabbit) | Cell Signalling | Cat. Nr. #4499S; RRID:AB_10544537 |
| anti-RecA (produced in rabbit) | abcam | Cat. Nr. ab63797; RRID:AB_1142554 |
| anti-GAPDH (D16H11) (HRP-conjugate, produced in rabbit) | Cell Signalling | Cat. Nr. #8884; RRID:AB_11129865 |
| anti-FLAG M2 (produced in mouse) | Sigma | Cat. Nr. F1804; RRID:AB_262044 |
| anti-RNA polymerase Sigma 70 (RpoD) [2G10] | Acris antibodies | Cat. Nr. GTX12088; RRID:AB_384272 |
| anti-LAMP1 (produced in rat, Alexa-488 conjugate) | abcam | Cat. Nr. ab24871; RRID:AB_2134490 |
| anti-LAMP1 (polyclonal, produced in rabbit) | Sigma | Cat. Nr. L1418; RRID:AB_477157 |
| anti-LAMP2 (polyclonal, produced in rabbit) | courtesy of M. Fukuda | N/A |
| anti-NPC1 (polyclonal, produced in rabbit) | Novus biologicals | Cat. Nr. NB400–148; RRID:AB_10001101 |
| anti-PDZD8 (amino acid residues 1101–1118), rabbit affinity purified | New England Peptide (custom) | N/A |
| anti-PDZD8 (polyclonal, produced in rabbit) | Sigma | Cat. Nr. HPA015716; RRID:AB_1855162 |
| anti-PDZD8 (polyclonal, produced in rabbit) | Sigma | Cat. Nr. HPA051610; RRID:AB_2681549 |
| anti-BAP31 (monoclonal, produced in mouse) | Invitrogen | Cat. Nr. MA3–002; RRID:AB_325095 |
| anti-PDI (produced in mouse) | Affinity Bioreagents | Cat. Nr. clone RL90 |
| anti-PDI (monoclonal, produced in mouse) | Stressgen | Cat. Nr. SPA-891; RRID:AB_2039450 |
| anti-TOM20 (monoclonal, clone F-10, produced in mouse) | Santa Cruz | Cat. Nr. sc-17764; RRID:AB_628381 |
| anti-Hsp27 (monoclonal, clone G31, produced in mouse) | Cell Signaling | Cat. Nr. #2402; RRID:AB_331761 |
| anti-calnexin (polyclonal, produced in rabbit) | Enzo | Cat. Nr. ADI-SPA-860; RRID:AB_10616095 |
| anti-lamin A (monoclonal, produced in mouse) | Cell Signaling | Cat. Nr. 133A2; RRID:AB_2800093 |
| secondary anti-rabbit (Alexa-680 coupled, produced in goat) | abcam | Cat. Nr. ab175773 |
| secondary anti-rat (HRP-conjugate, produced in rabbit) | abcam | Cat. Nr. ab6734; RRID:AB_955450 |
| secondary anti-mouse (HRP-conjugate, produced in goat) | Sigma | Cat. Nr. HVZ-A4416–1ML |
| secondary anti-rabbit (HRP-conjugate, produced in donkey) | Sigma/GE | Cat. Nr. NA934–1ML; RRID:AB_772206 |
| anti-rabbit IgG horseradish peroxidase | Cell Signalling | Cat. Nr. #7071; RRID:AB_2099234 |
| anti-GFP (monoclonal, clone 3E6, produced in mouse) | Molecular Probes | Cat. Nr. mAb 3E6; RRID:AB_2313858 |
| anti-GFP (polyclonal, produced in rabbit) | Molecular Probes | Cat. Nr. A-11122; RRID:AB_221569 |
| rat monoclonal anti-HA high affinity, clone 3F10 | Roche | Cat. Nr. #3F10; RRID:AB_2314622 |
| mouse monoclonal anti--HA.11 | BioLegend | N/A |
| mouse monoclonal anti-myc, clone 9B11 | Cell Signaling | Cat. Nr. #2040; RRID:AB_2148465 |
| Bacterial and virus strains | ||
| TOP10 F- mcrA Δ(mrr-hsdRMS-mcrBC) φ80lacZΔM15 ΔlacX74 nupG recA1 araD139 Δ(ara-leu)7697 galE15 galK16 rpsL(StrR) endA1 λ | Invitrogen | N/A |
| Rosetta(DE3) plysRare | Novagen | N/A |
| wild type Salmonella enterica serovar Typhimurium 14028s | Porwollik et al., 2014 | N/A |
| STm 14028S gogB:STF-kan | this study | N/A |
| STm 14028S sseK1:STF-kan | this study | N/A |
| STm 14028S sseJ:STF-kan | this study | N/A |
| STm 14028S ΔccdAB::Cm, sifA:STF | this study | N/A |
| STm 14028S pipB:STF-kan | this study | N/A |
| STm 14028S pipB2:STF-kan | this study | N/A |
| STm 14028S sifB:STF-kan | this study | N/A |
| STm 14028S slrP:STF-kan | this study | N/A |
| STm 14028S sopD2:STF-kan | this study | N/A |
| STm 14028S spvB:STF-kan | this study | N/A |
| STm 14028S spvC:STF-kan | this study | N/A |
| STm 14028S srgE:STF-kan | this study | N/A |
| STm 14028S sseF:STF-kan | this study | N/A |
| STm 14028S sseG:STF-kan | this study | N/A |
| STm 14028S sseI:STF-kan | this study | N/A |
| STm 14028S sipA:STF-kan | this study | N/A |
| STm 14028S sopB:STF-kan | this study | N/A |
| STm 14028S sseK2:STF-kan | this study | N/A |
| STm 14028S sseL:STF-kan | this study | N/A |
| STm 14028S sspH1:STF-kan | this study | N/A |
| STm 14028S sspH2:STF-kan | this study | N/A |
| STm 14028S steA:STF-kan | this study | N/A |
| STm 14028S steB:STF-kan | this study | N/A |
| STm 14028S steC:STF-kan | this study | N/A |
| STm 14028S sptP:STF-kan | this study | N/A |
| STm 14028S steE:STF-kan | this study | N/A |
| STm 14028S cigR:STF-kan | this study | N/A |
| STm 14028S avrA:STF-kan | this study | N/A |
| STm 14028S sipB:STF-kan | this study | N/A |
| STm 14028S sipC:STF-kan | this study | N/A |
| STm 14028S sopA:STF-kan | this study | N/A |
| STm 14028S steD:STF-kan | this study | N/A |
| STm 14028S ΔsseJ:: | this study | N/A |
| STm 14028S ΔsseL:: | this study | N/A |
| STm 14028S ΔsteC:: | this study | N/A |
| STm 14028S ΔsseJ::kan, retransduced into wildtype using P22 | Porwollik et al., 2014 | N/A |
| STm 14028S ΔsseL::kan, retransduced into wildtype using P22 | Porwollik et al., 2014 | N/A |
| STm 14028S ΔsteC::kan, retransduced into wildtype using P22 | Porwollik et al., 2014 | N/A |
| STm 14028S ΔsseJ::ΔsseL:: | this study | N/A |
| STm 14028S ΔssaV::kan, retransduced into wildtype using P22 | Porwollik et al., 2014 | N/A |
| STm 14028S ΔprgK::kan, retransduced into wildtype using P22 | Porwollik et al., 2014 | N/A |
| STm 14028S ΔsifA::kan, retransduced into wildtype using P22 | Porwollik et al., 2014 | N/A |
| STm 14028S, pFCcGi | this study | N/A |
| STm 14028S ΔsseJ::, pFCcGi | this study | N/A |
| STm 14028S ΔsseL::, pFCcGi | this study | N/A |
| STm 14028S ΔsteC::, pFCcGi | this study | N/A |
| STm 14028S ΔsseJ::kan, pFCcGi | this study | N/A |
| STm 14028S ΔsseJ::kan, pFCcGi | this study | N/A |
| STm 14028S ΔsseL::kan, pFCcGi | this study | N/A |
| STm 14028S ΔsseL::kan, pFCcGi | this study | N/A |
| STm 14028S ΔsteC::kan, pFCcGi | this study | N/A |
| STm 14028S ΔsteC::kan, pFCcGi | this study | N/A |
| STm 14028S ΔsseJ::ΔsseL::, pFCcGi | this study | N/A |
| STm 14028S ΔssaV::kan, pFCcGi | this study | N/A |
| STm 14028S ΔprgK::kan, pFCcGi | this study | N/A |
| STm 14028S ΔsifA::kan, pFCcGi | this study | N/A |
| SL1344 wild type | Hoiseth and Stocker 1981 | N/A |
| STm SL1344 ΔpipB | Knodler et al., 2002 | N/A |
| STm SL1344 ΔpipB pPipB-2HA | Knodler et al., 2002 | N/A |
| STm SL1344 ΔpipB glmS::Ptrc-mCherryST::FRT | this study | N/A |
| STm SL1344 ΔpipB glmS::Ptrc-mCherryST::FRT pPipB-2HA | this study | N/A |
| STm SL1344 ΔpipB glmS::Ptrc-mCherryST::FRT pPipB(Δ270–291)-2HA | this study | N/A |
| STm SL1344 ΔpipB2 | Knodler et al., 2003 | N/A |
| STm SL1344 ΔpipB2 pPipB2–2HA | Knodler et al., 2003 | N/A |
| Deposited data | ||
| Additional and original data for Western Blots, limma analyses, all plots and other MS runs | this study | Mendeley Data DOI: 10.17632/xjb24h7s8j.1 |
| All original proteomic data | this study | PRIDE repository: PXD018375 |
| STRING DB v11 | Szklarczyk et al., 2019 | https://string-db.org/ |
| UniProt (UP000005640, UP000000589, UP000002695) | The UniProt Consortium, 2021 | https://www.uniprot.org/ |
| Experimental models: cell lines | ||
| HeLa (Wildtype) | ATCC | ATCC CCL-2; RRID:CVCL_0030 |
| HeLa (NPC1-K.O.) | provided by Dr. Willem Annaert (VIB, KU-Leuven) | N/A |
| RAW264.7 (Wildtype) | ATCC | ATCC TIB-71; RRID:CVCL_0493 |
| 3T3 (Wildtype) | provided by Prof. Dr. Klemens Rottner | N/A |
| 3T3 (FMNL2/3-K.O.) | provided by Prof. Dr. Klemens Rottner | N/A |
| pBMDM (Wildtype mice) | bone marrow provided by Prof. Dr. Wolf-Dietrich Hardt (ETH) | N/A |
| Oligonucleotides | ||
| See Table S7 for a full list of oligonucleotides used in this study. Further information on all oligos is provided on Mendeley Data (DOI: 10.17632/xjb24h7s8j.1) | ||
| Recombinant DNA | ||
| pFCcGi: Constitutive expression of mCherry(FC), AmpR | Figueira et al., 2013 | RRID:Addgene_59324 |
| pGEM-T Easy: AmpR, T/A cloning vector | Invitrogen | Cat. Nr. PR-A1360 |
| pQE30: AmpR | Qiagen | N/A |
| pMZ2: plasmid containing 2x Myc-TEV-FLAG tag and KanR gene from pKD4 cloned into the EcoRI/HindIII site of pQE-30, AmpR | this work | N/A |
| pJSP1: pGEM-Teasy backbone containing 2x STREP-TEV-3xFLAG tag and KanR gene from pKD4, AmpR | this work | N/A |
| pKD45: plasmid carrying neo-ccdB cassette, R6K ori | Datsenko & Wanner 2000 | N/A |
| pKD3: plasmid carrying FRT-cat-FRT cassette, CmR, AmpR | Datsenko & Wanner 2000 | RRID:Addgene_45604 |
| pKD4: plasmid carrying FRT-neo-FRT cassette, KanR, AmpR | Datsenko & Wanner 2000 | RRID:Addgene_45605 |
| pKD46: λ Red recombinase expression vector, AmpR | Datsenko & Wanner 2000 | N/A |
| pCP20: Plasmid expressing FLP recombinase, AmpRs, ts rep | Datsenko & Wanner 2000 | N/A |
| pACYC184: CmR, TetR | New England Biolabs | GenBank Accession #: X06403 |
| pPipB-2HA: plasmid expressing c-terminal HA tagged PipB | Knodler et al. 2003 | N/A |
| pPipB2–2HA: plasmid expressing c-terminal HA tagged PipB2 | Knodler et al. 2003 | N/A |
| EGFP-PipB: expression of GFP tagged PipB | this work | N/A |
| EGFP-PipB(Δ270–291): expression of GFP tagged PipB(Δ270–291) | this work | N/A |
| EGFP-PipB2: expression of GFP tagged PipB2 | Knodler and Steele-Mortimer, 2005 | N/A |
| pKozak-PDZD8-myc: ectopic expression of PDZD8 expressing a c-terminal myc tag | this work | N/A |
| pCMV-Tag 5A: mammalina expression vector, KanR | Stratagene | N/A |
| pGAD424: generation of gene fusions for Y2H | Clontech | N/A |
| pGAD424-PipB: plasmid expressing PipB for Y2H | this work | N/A |
| pGAD424-PipB(1–281): plasmid expressing PipB(1–281) for Y2H | this work | N/A |
| pGAD424-PipB(1–271): plasmid expressing PipB(1–271) for Y2H | this work | N/A |
| pGAD424-PipB(1–188): plasmid expressing PipB(1–188) for Y2H | this work | N/A |
| pGAD424-PipB(189–291): plasmid expressing PipB(189–291) for Y2H | this work | N/A |
| pGBT9: generation of gene fusions for Y2H | Clontech | N/A |
| pGBT9-PDZD8: plasmid expressing PDZD8 for Y2H | this work | N/A |
| pGBT9-PDZD8(Δ930–1154): plasmid expressing PDZD8(Δ930–1154) for Y2H | this work | N/A |
| pGBT9-PDZD8(Δ1–338): plasmid expressing PDZD8(Δ1–338) for Y2H | this work | N/A |
| pGBT9-PDZD8ΔPDZ: plasmid expressing PDZD8ΔPDZ for Y2H | this work | N/A |
| pGBT9-PDZD8(Δ494–814): plasmid expressing PDZD8(Δ494–814) for Y2H | this work | N/A |
| pGBT9-PDZD8ΔC1: plasmid expressing PDZD8ΔC1 for Y2H | this work | N/A |
| Software and algorithms | ||
| Inkscape v1.0.2 | Free Software Foundation, Inc. | https://inkscape.org |
| GraphPad Prism v7 | GraphPad Software, San Diego, California USA | https://www.graphpad.com/scientific-software/prism/ |
| Cell Profiler v3.0.0 | McQuin et al. 2018 | https://cellprofiler.org/ |
| cytoscape v3.7.2 | Shannon et al. 2003 | https://cytoscape.org/ |
| clueGO plug-in in cytoscape (v2.5.2) | Bindea et al. 2009 | httphttp://apps.cytoscape.org/apps/cluego |
| ImageJ v1.51n | Schneider et al. 2012 | https://imagej.net/Welcome |
| MaxQuant v1.6.2.3 | Cox and Mann, 2008 | https://www.maxquant.org/ |
| IsobarQuant | Franken et al., 2015 | https://github.com/protcode/isob |
| Mascot v2.2.07 | Perkins et al. 1999 | https://www.matrixscience.com/ |
| R programming language (ISBN 3–900051-07–0) | R Core team, 2017 | https://www.r-project.org/ |