KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| S9.6 DNA:RNA Hybrid antibody | Millipore | MABE1095 |
| S9.6 DNA:RNA Hybrid antibody | Kerafast | ENH001 |
| DnaC Antibody | (Smits et al., 2010) | N/A |
| Chemicals, Peptides, and Recombinant Proteins | ||
| EcoRV-HF | NEB | R3195 |
| PstI-HF | NEB | R3140 |
| HindIII-HF | NEB | R3104 |
| DpnI | Thermo | FD1703 |
| XhoI | Thermo | FD0694 |
| EcoRI | Thermo | FD0274 |
| HindIII | Thermo | FD0504 |
| EagI | Thermo | FD0334 |
| NheI | Thermo | FD0974 |
| SphI | Thermo | FD0604 |
| DNase I | Thermo | 89836 |
| Proteinase K | Qiagen | 19133 |
| Protein A Sepharose beads | GE Healthcare | 17-0780-01 |
| Sephadex G-50 | GE | 17004201 |
| SeaKem LE agarose | Thermo | 50002 |
| Recombinant Human IFN-Gamma | PeproTech | 300-02 |
| Critical Commercial Assays | ||
| Ovation Complete Prokaryotic RNA-Seq kit | Nugen | 0326 |
| Nextera XT DNA Library Preparation Kit | Illumina | (FC-131-1024) |
| Deposited Data | ||
| All fastq files and descriptions uploaded to Sequence Read Archive | NCBI SRA | Bioproject: SUB2307064 |
| Experimental Models: Cell Lines | ||
| Immortalized bone marrow macrophages | (Sureka et al., 2014) | N/A |
| TIB73 murine hepatocytes | (Sureka et al., 2014) | N/A |
| Experimental Models: Organisms/Strains | ||
| B. subtilis trpC2 pheA1 | (Brehm et al., 1973) | HM1 |
| B. subtilis hisC952, metB5, leuC427, SPβsens, xin−1, amyE::Pspank(hy)-hisC952 (HO) specR | (Paul et al., 2013) | HM419 |
| B. subtilis hisC952, metB5, leuC427, SPβsens, xin−1, amyE::Pspank(hy)-hisC952 (CD) specR | (Paul et al., 2013) | HM420 |
| B. subtilis trpC2 rnhB::mls | Bacillus Stock Center | HM710 |
| B. subtilis trpC2 rnhC::mls | Bacillus Stock Center | HM711 |
| B. subtilis amyE::Pspank(hy)-lacZ (HO) specR, trpC2 pheA1 | This study | HM1300 |
| B. subtilis amyE::Pspank(hy)-lacZ (CD) specR, trpC2 pheA1 | This study | HM1416 |
| B. subtilis trpC2 ypeP::mls | Bacillus Stock Center | HM1907 |
| B. subtilis trpC2 ypdQ::mls | Bacillus Stock Center | HM1908 |
| B. subtilis rnhB::mls amyE::Pspank(hy)-lacZ (HO) specR, trpC2 pheA1 | This study | HM2041 |
| B. subtilis rnhB::mls amyE::Pspank(hy)-lacZ (CD) specR, trpC2 pheA1 | This study | HM2042 |
| B. subtilis rnhC::mls amyE::Pspank(hy)-lacZ (HO) specR, trpC2 pheA1 | This study | HM2043 |
| B. subtilis rnhC::mls amyE::Pspank(hy)-lacZ (CD) specR, trpC2 pheA1 | This study | HM2044 |
| B. subtilis amyE::Pspank(hy)-luxABCDE (HO) specR, trpC2 pheA1 | This study | HM2195 |
| B. subtilis amyE::Pspank(hy)-luxABCDE (CD) specR, trpC2 pheA1 | This study | HM2197 |
| B. subtilis amyE::Pspank(hy)-hisC952 (HO) hisC952, metB5, leuC427, xin-1, SPβsens thrC::Pspank(hy)-rnhC | This study | HM2482 |
| B. subtilis amyE::Pspank(hy)-hisC952 (CD) hisC952, metB5, leuC427, xin-1, SPβsens thrC::Pspank(hy)-rnhC | This study | HM2483 |
| B. subtilis rnhC::mls trpC2 pheA1 | This study | HM2655 |
| B. subtilis rnhC::mls amyE::Pspank(hy)-lacZ (HO) specR lacA::PrnhC-rnhC tetR, trpC2 pheA1 | This study | HM2656 |
| B. subtilis rnhC::mls amyE::Pspank(hy)-lacZ (CD) specR lacA::PrnhC-rnhC tetR, trpC2 pheA1 | This study | HM2657 |
| B. subtilis rnhC::mls amyE::Pspank(hy)-luxABCDE (HO) specR, trpC2 pheA1 | This study | HM2658 |
| B. subtilis rnhC::mls amyE::Pspank(hy)-luxABCDE (CD) specR, trpC2 pheA1 | This study | HM2659 |
| B. subtilis rnhC::mls amyE::Pspank(hy)-luxABCDE (HO) specR, lacA::PrnhC-rnhC tetR trpC2 pheA1 | This study | HM2706 |
| B. subtilis rnhC::mls amyE::Pspank(hy)-luxABCDE (CD) specR, lacA::PrnhC-rnhC tetR trpC2 pheA1 | This study | HM2707 |
| B. subtilis ypeP::mls amyE::Pspank(hy)-lacZ (HO) specR, trpC2 pheA1 | This study | HM2781 |
| B. subtilis ypeP::mls amyE::Pspank(hy)-lacZ (CD) specR, trpC2 pheA1 | This study | HM2782 |
| B. subtilis ypdQ::mls amyE::Pspank(hy)-lacZ (HO) specR, trpC2 pheA1 | This study | HM2783 |
| B. subtilis ypdQ::mls amyE::Pspank(hy)-lacZ (CD) specR, trpC2 pheA1 | This study | HM2784 |
| B. subtilis rnhC::mls amyE::Pspank(hy)-lacZ (HO) specR lacA::PrnhC-rnhC(E234A) tetR, trpC2 pheA1 | This study | HM3208 |
| B. subtilis rnhC::mls amyE::Pspank(hy)-lacZ (CD) specR lacA::PrnhC-rnhC(E234A) tetR, trpC2 pheA1 | This study | HM3209 |
| Listeria monocytogenes 10403S strepR | Gift from Dr. Joshua Woodward | HM3274 |
| Listeria monocytogenes 10403S ΔrnhC strepR | This study | HM3275 |
| Mouse: C57BL/6J | Jackson Laboratory | 000664 |
| Recombinant DNA | ||
| pDR111 | Gift from Dr. David Rudner | pDR111 |
| pCAL838 | Guérout-Fleury, Gene. 1996 | pCAL838 |
| pAH60 | Gift from Dr. Richard Losick | pAH60 |
| pMMB752 | Gift from Dr. Alan Grossman | pMMB752 |
| pKSV7 | Gift from Dr. Joshua Woodward | pKSV7 |
| pHM64 | This study | pHM64 |
| pHM170 | This study | pHM170 |
| pHM181 | This study | pHM181 |
| pHM271 | This study | pHM271 |
| pHM321 | This study | pHM321 |
| pHM506 | This study | pHM506 |
| pHM568 | This study | pHM568 |
| Sequence-Based Reagents | ||
| Primer sequences provided in Table S3 | N/A | N/A |
| Software and Algorithms | ||
| SAMtools | Li et al. 2009 | N/A |
| Bowtie 2 | Langmead and Salzberg, 2012 | N/A |
| Prism 7 | Graphpad | N/A |
| DeepTools | Ramírez et al., 2014 | N/A |
| CLC Genomics Workbench | N/A | N/A |
| ImageJ | N/A | N/A |
| Other | ||
| GeneJET PCR Purification Kit | Thermo | K0701 |
| iTaq Universal SYBR Green master mix | Bio-Rad | 1725121 |
| iScript Supermix | Bio-Rad | 1708840 |
| GeneJET RNA Purification Kit | Thermo | K0731 |
| GeneJET Genomic DNA purification Kit | Thermo | K0722 |